22 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8ed926ee0b52/
Changeset: 8ed926ee0b52
User: jgoecks
Date: 2013-08-21 19:01:53
Summary: Enhancements to Tool client-server interactions: (a) use DictifiableMixin to dictify toolbox, tools, and tool inputs + outputs; (b) integrate code from visual analytics module with tool/parameter code base and remove VA module; (c) harmonize class names for tool panel on server and client side; (d) update client-side tool panel code and trackster code to work with server-side enhancements. Pack scripts.
Affected #: 18 files
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1508,7 +1508,7 @@
return msg
-class HistoryDatasetAssociation( DatasetInstance, UsesAnnotations ):
+class HistoryDatasetAssociation( DatasetInstance, DictifiableMixin, UsesAnnotations ):
"""
Resource class that creates a relation between a dataset and a user history.
"""
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/model/item_attrs.py
--- a/lib/galaxy/model/item_attrs.py
+++ b/lib/galaxy/model/item_attrs.py
@@ -193,7 +193,7 @@
try:
visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' )
except AttributeError:
- raise Exception( 'Unknown API view: %s' % view )
+ raise Exception( 'Unknown DictifiableMixin view: %s' % view )
for key in visible_keys:
try:
item = self.__getattribute__( key )
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -59,6 +59,7 @@
from galaxy.util.template import fill_template
from galaxy.web import url_for
from galaxy.web.form_builder import SelectField
+from galaxy.model.item_attrs import DictifiableMixin
from tool_shed.util import shed_util_common
from .loader import load_tool, template_macro_params
@@ -92,7 +93,7 @@
class ToolNotFoundException( Exception ):
pass
-class ToolBox( object ):
+class ToolBox( object, DictifiableMixin ):
"""Container for a collection of tools"""
def __init__( self, config_filenames, tool_root_dir, app ):
@@ -701,7 +702,7 @@
"""
return self.app.model.context
- def to_dict( self, trans, in_panel=True, **kwds ):
+ def dictify( self, trans, in_panel=True, **kwds ):
"""
Dictify toolbox.
"""
@@ -722,11 +723,11 @@
# Produce panel.
rval = []
for elt in panel_elts:
- rval.append( elt.to_dict( trans, for_link=True ) )
+ rval.append( elt.dictify( trans, link_details=True ) )
else:
tools = []
for id, tool in self.tools_by_id.items():
- tools.append( tool.to_dict( trans, for_link=True ) )
+ tools.append( tool.dictify( trans, link_details=True ) )
rval = tools
return rval
@@ -787,11 +788,14 @@
-class ToolSection( object ):
+class ToolSection( object, DictifiableMixin ):
"""
A group of tools with similar type/purpose that will be displayed as a
group in the user interface.
"""
+
+ dict_collection_visible_keys = ( 'id', 'name', 'version' )
+
def __init__( self, elem=None ):
f = lambda elem, val: elem is not None and elem.get( val ) or ''
self.name = f( elem, 'name' )
@@ -807,27 +811,33 @@
copy.elems = self.elems.copy()
return copy
- def to_dict( self, trans, for_link=False ):
+ def dictify( self, trans, link_details=False ):
""" Return a dict that includes section's attributes. """
+
+ section_dict = super( ToolSection, self ).dictify()
section_elts = []
for key, val in self.elems.items():
- section_elts.append( val.to_dict( trans, for_link=for_link ) )
- return { 'type': 'section', 'id': self.id, 'name': self.name, 'version': self.version, 'elems': section_elts }
+ if isinstance( val, ToolSectionLabel ):
+ section_elts.append( val.dictify() )
+ else:
+ section_elts.append( val.dictify( trans, link_details=link_details ) )
+ section_dict[ 'elems' ] = section_elts
-class ToolSectionLabel( object ):
+ return section_dict
+
+class ToolSectionLabel( object, DictifiableMixin ):
"""
A label for a set of tools that can be displayed above groups of tools
and sections in the user interface
"""
+
+ dict_collection_visible_keys = ( 'id', 'text', 'version' )
+
def __init__( self, elem ):
self.text = elem.get( "text" )
self.id = elem.get( "id" )
self.version = elem.get( "version" ) or ''
- def to_dict( self, trans, **kwargs ):
- """ Return a dict that includes label's attributes. """
- return { 'type': 'label', 'id': self.id, 'name': self.text, 'version': self.version }
-
class DefaultToolState( object ):
"""
Keeps track of the state of a users interaction with a tool between
@@ -874,7 +884,7 @@
self.rerun_remap_job_id = None
self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True )
-class ToolOutput( object ):
+class ToolOutput( object, DictifiableMixin ):
"""
Represents an output datasets produced by a tool. For backward
compatibility this behaves as if it were the tuple::
@@ -882,6 +892,8 @@
(format, metadata_source, parent)
"""
+ dict_collection_visible_keys = ( 'name', 'format', 'label', 'hidden' )
+
def __init__( self, name, format=None, format_source=None, metadata_source=None,
parent=None, label=None, filters = None, actions = None, hidden=False ):
self.name = name
@@ -912,14 +924,6 @@
def __iter__( self ):
return iter( ( self.format, self.metadata_source, self.parent ) )
- def to_dict( self ):
- return {
- 'name': self.name,
- 'format': self.format,
- 'label': self.label,
- 'hidden': self.hidden
- }
-
class ToolRequirement( object ):
"""
Represents an external requirement that must be available for the tool to run (for example, a program, package, or library).
@@ -930,13 +934,14 @@
self.type = type
self.version = version
-class Tool( object ):
+class Tool( object, DictifiableMixin ):
"""
Represents a computational tool that can be executed through Galaxy.
"""
tool_type = 'default'
default_tool_action = DefaultToolAction
+ dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' )
def __init__( self, config_file, root, app, guid=None, repository_id=None ):
"""Load a tool from the config named by `config_file`"""
@@ -1225,7 +1230,6 @@
# Trackster configuration.
trackster_conf = root.find( "trackster_conf" )
if trackster_conf is not None:
- from galaxy.visualization.genome.visual_analytics import TracksterConfig
self.trackster_conf = TracksterConfig.parse( trackster_conf )
else:
self.trackster_conf = None
@@ -2944,66 +2948,29 @@
self.sa_session.flush()
return primary_datasets
- def to_dict( self, trans, for_link=False, for_display=False ):
+ def dictify( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
# Basic information
- tool_dict = { 'id': self.id, 'name': self.name,
- 'version': self.version, 'description': self.description }
-
- if for_link:
- # Create tool link.
+ tool_dict = super( Tool, self ).dictify()
+
+ # Add link details.
+ if link_details:
+ # Add details for creating a hyperlink to the tool.
if not self.tool_type.startswith( 'data_source' ):
link = url_for( '/tool_runner', tool_id=self.id )
else:
link = url_for( self.action, **self.get_static_param_values( trans ) )
# Basic information
- tool_dict.update( { 'type': 'tool', 'link': link,
+ tool_dict.update( { 'link': link,
'min_width': self.uihints.get( 'minwidth', -1 ),
'target': self.target } )
- if for_display:
- # Dictify inputs.
- inputs = []
- for name, input in self.inputs.items():
- param_dict = { 'name' : name, 'label' : input.label }
- if isinstance( input, DataToolParameter ):
- param_dict.update( { 'type' : 'data', 'html' : urllib.quote( input.get_html( trans ) ) } )
- elif isinstance( input, SelectToolParameter ):
- # Get options, value.
- options = input.get_options( trans, [] )
- value = options[0][1]
- for option in options:
- if option[2]:
- # Found selected option.
- value = option[1]
-
- # Pack input.
- param_dict.update( { 'type' : 'select',
- 'html' : urllib.quote( input.get_html( trans ) ),
- 'options': options,
- 'value': value
- } )
- elif isinstance( input, Conditional ):
- # TODO.
- pass
- elif isinstance( input, ( IntegerToolParameter, FloatToolParameter ) ):
- param_dict.update( { 'type' : 'number', 'init_value' : input.value,
- 'html' : urllib.quote( input.get_html( trans ) ),
- 'min': input.min,
- 'max': input.max,
- 'value': input.value
- } )
- else:
- param_dict.update( { 'type' : '??', 'init_value' : input.value, \
- 'html' : urllib.quote( input.get_html( trans ) ) } )
- inputs.append( param_dict )
-
- tool_dict[ 'inputs' ] = inputs
-
- # Dictify outputs.
- pass
+ # Add input and output details.
+ if io_details:
+ tool_dict[ 'inputs' ] = [ input.dictify( trans ) for input in self.inputs.values() ]
+ tool_dict[ 'outputs' ] = [ output.dictify() for output in self.outputs.values() ]
return tool_dict
@@ -3240,6 +3207,31 @@
# ---- Utility classes to be factored out -----------------------------------
+class TracksterConfig:
+ """ Trackster configuration encapsulation. """
+
+ def __init__( self, actions ):
+ self.actions = actions
+
+ @staticmethod
+ def parse( root ):
+ actions = []
+ for action_elt in root.findall( "action" ):
+ actions.append( SetParamAction.parse( action_elt ) )
+ return TracksterConfig( actions )
+
+class SetParamAction:
+ """ Set parameter action. """
+
+ def __init__( self, name, output_name ):
+ self.name = name
+ self.output_name = output_name
+
+ @staticmethod
+ def parse( elt ):
+ """ Parse action from element. """
+ return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) )
+
class BadValue( object ):
def __init__( self, value ):
self.value = value
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2,7 +2,7 @@
Basic tool parameters.
"""
-import logging, string, sys, os, os.path
+import logging, string, sys, os, os.path, urllib
from elementtree.ElementTree import XML, Element
from galaxy import config, datatypes, util
from galaxy.web import form_builder
@@ -12,16 +12,19 @@
import validation, dynamic_options
# For BaseURLToolParameter
from galaxy.web import url_for
+from galaxy.model.item_attrs import DictifiableMixin
import galaxy.model
log = logging.getLogger(__name__)
-class ToolParameter( object ):
+class ToolParameter( object, DictifiableMixin ):
"""
Describes a parameter accepted by a tool. This is just a simple stub at the
moment but in the future should encapsulate more complex parameters (lists
of valid choices, validation logic, ...)
"""
+ dict_collection_visible_keys = ( 'name', 'type', 'label', 'help' )
+
def __init__( self, tool, param, context=None ):
self.tool = tool
self.refresh_on_change = False
@@ -167,6 +170,15 @@
for validator in self.validators:
validator.validate( value, history )
+ def dictify( self, trans, view='collection', value_mapper=None ):
+ """ Dictify tool parameter. This can be overridden by subclasses. """
+
+ tool_dict = super( ToolParameter, self ).dictify()
+ tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) )
+ if hasattr( self, 'value' ):
+ tool_dict[ 'value' ] = self.value
+ return tool_dict
+
@classmethod
def build( cls, tool, param ):
"""Factory method to create parameter of correct type"""
@@ -223,6 +235,9 @@
...
ValueError: An integer is required
"""
+
+ dict_colletion_visible_keys = ToolParameter.dict_collection_visible_keys + ( 'min', 'max' )
+
def __init__( self, tool, elem ):
TextToolParameter.__init__( self, tool, elem )
if self.value:
@@ -276,7 +291,7 @@
return int( self.value )
else:
return None
-
+
class FloatToolParameter( TextToolParameter ):
"""
Parameter that takes a real number value.
@@ -293,6 +308,9 @@
...
ValueError: A real number is required
"""
+
+ dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ( 'min', 'max' )
+
def __init__( self, tool, elem ):
TextToolParameter.__init__( self, tool, elem )
self.min = elem.get( 'min' )
@@ -854,6 +872,24 @@
else:
return []
+ def dictify( self, trans, view='collection', value_mapper=None ):
+ d = super( SelectToolParameter, self ).dictify( trans )
+
+ # Get options, value.
+ options = self.get_options( trans, [] )
+ value = options[0][1]
+ for option in options:
+ if option[2]:
+ # Found selected option.
+ value = option[1]
+
+ d.update( {
+ 'options': options,
+ 'value': value
+ } )
+ return d
+
+
class GenomeBuildParameter( SelectToolParameter ):
"""
Select list that sets the last used genome build for the current history
@@ -1680,7 +1716,7 @@
if call_attribute:
ref = ref()
return ref
-
+
class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ):
"""
Hidden parameter that behaves as a DataToolParameter. As with all hidden
@@ -1689,6 +1725,7 @@
def __init__( self, tool, elem ):
DataToolParameter.__init__( self, tool, elem )
self.value = "None"
+ self.type = "hidden_data"
def get_initial_value( self, trans, context ):
return None
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/tools/parameters/grouping.py
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -15,30 +15,44 @@
from galaxy.util import sanitize_for_filename
from galaxy.util.bunch import Bunch
from galaxy.util.expressions import ExpressionContext
+from galaxy.model.item_attrs import DictifiableMixin
-class Group( object ):
+class Group( object, DictifiableMixin ):
+
+ dict_collection_visible_keys = ( 'name', 'type' )
+
def __init__( self ):
self.name = None
+ self.type = 'group'
+
@property
def visible( self ):
return True
+
def value_to_basic( self, value, app ):
"""
Convert value to a (possibly nested) representation using only basic
types (dict, list, tuple, str, unicode, int, long, float, bool, None)
"""
return value
+
def value_from_basic( self, value, app, ignore_errors=False ):
"""
Convert a basic representation as produced by `value_to_basic` back
into the preferred value form.
"""
return value
+
def get_initial_value( self, trans, context ):
"""
Return the initial state/value for this group
"""
raise TypeError( "Not implemented" )
+
+ def dictify( self, trans, view='collection', value_mapper=None ):
+ # TODO: need to dictify conditions.
+ group_dict = super( Group, self ).dictify( view=view, value_mapper=value_mapper )
+ return group_dict
class Repeat( Group ):
type = "repeat"
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/visualization/genome/visual_analytics.py
--- a/lib/galaxy/visualization/genome/visual_analytics.py
+++ /dev/null
@@ -1,82 +0,0 @@
-import urllib
-
-from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter
-from galaxy.tools.parameters.dynamic_options import DynamicOptions
-
-class TracksterConfig:
- """ Trackster configuration encapsulation. """
-
- def __init__( self, actions ):
- self.actions = actions
-
- @staticmethod
- def parse( root ):
- actions = []
- for action_elt in root.findall( "action" ):
- actions.append( SetParamAction.parse( action_elt ) )
- return TracksterConfig( actions )
-
-class SetParamAction:
- """ Set parameter action. """
-
- def __init__( self, name, output_name ):
- self.name = name
- self.output_name = output_name
-
- @staticmethod
- def parse( elt ):
- """ Parse action from element. """
- return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) )
-
-def get_dataset_job( hda ):
- # Get dataset's job.
- job = None
- for job_output_assoc in hda.creating_job_associations:
- job = job_output_assoc.job
- break
- return job
-
-def get_tool_def( trans, hda ):
- """ Returns definition of an interactive tool for an HDA. """
-
- #FIXME: use tools.to_dict rather than custom code here.
-
- job = get_dataset_job( hda )
- # TODO: could use this assertion to provide more information.
- # assert job is not None, 'Requested job has not been loaded.'
- if not job:
- return None
- tool = trans.app.toolbox.get_tool( job.tool_id )
- # TODO: could use this assertion to provide more information.
- # assert tool is not None, 'Requested tool has not been loaded.'
- if not tool:
- return None
-
- # Tool must have a Trackster configuration.
- if not tool.trackster_conf:
- return None
-
- # Get list of tool parameters that can be interactively modified.
- tool_params = []
- tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] )
- tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True )
- for name, input in tool.inputs.items():
- if type( input ) == IntegerToolParameter or type( input ) == FloatToolParameter:
- param_dict = { 'name' : name, 'label' : input.label, \
- 'value' : tool_param_values.get( name, input.value ), \
- 'type' : 'number', 'init_value' : input.value,
- 'html' : urllib.quote( input.get_html() ) }
- if input.min:
- param_dict['min'] = input.min
- if input.max:
- param_dict['max'] = input.max
- tool_params.append( param_dict )
- elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions:
- tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \
- 'value' : tool_param_values.get( name, '' ), \
- 'html' : urllib.quote( input.get_html() ) } )
-
- # If tool has parameters that can be interactively modified, return tool.
- if len( tool_params ) != 0:
- return { 'id': tool.id, 'name' : tool.name, 'inputs' : tool_params }
- return None
\ No newline at end of file
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/visualization/genomes.py
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -73,7 +73,7 @@
self.len_file = len_file
self.twobit_file = twobit_file
- def to_dict( self, num=None, chrom=None, low=None ):
+ def dictify( self, num=None, chrom=None, low=None ):
"""
Returns representation of self as a dictionary.
"""
@@ -289,7 +289,7 @@
# Set up return value or log exception if genome not found for key.
rval = None
if genome:
- rval = genome.to_dict( num=num, chrom=chrom, low=low )
+ rval = genome.dictify( num=num, chrom=chrom, low=low )
else:
log.exception( 'genome not found for key %s' % dbkey )
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -32,12 +32,12 @@
from galaxy.model.orm import eagerload, eagerload_all
from galaxy.security.validate_user_input import validate_publicname
from galaxy.util.sanitize_html import sanitize_html
+from galaxy.model.item_attrs import DictifiableMixin
from galaxy.datatypes.interval import ChromatinInteractions
from galaxy.datatypes.data import Text
-from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation
-from galaxy.visualization.genome.visual_analytics import get_tool_def
+from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation,HistoryDatasetAssociation
from galaxy.datatypes.display_applications import util as da_util
from galaxy.datatypes.metadata import FileParameter
@@ -704,6 +704,15 @@
return changed
+ def get_hda_job( self, hda ):
+ # Get dataset's job.
+ job = None
+ for job_output_assoc in hda.creating_job_associations:
+ job = job_output_assoc.job
+ break
+ return job
+
+
class UsesLibraryMixin:
@@ -1105,6 +1114,37 @@
encoded_id = trans.security.encode_id( vis.id )
return { "vis_id": encoded_id, "url": url_for( controller='visualization', action=vis.type, id=encoded_id ) }
+ def get_tool_def( self, trans, hda ):
+ """ Returns definition of an interactive tool for an HDA. """
+
+ job = self.get_hda_job( hda )
+ if not job:
+ return None
+ tool = trans.app.toolbox.get_tool( job.tool_id )
+ if not tool:
+ return None
+
+ # Tool must have a Trackster configuration.
+ if not tool.trackster_conf:
+ return None
+
+ # Get tool definition and add input values from job.
+ tool_dict = tool.dictify( trans, io_details=True )
+ inputs_dict = tool_dict[ 'inputs' ]
+ tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] )
+ tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True )
+ for t_input in inputs_dict:
+ # Add value to tool.
+ if 'name' in t_input:
+ name = t_input[ 'name' ]
+ if name in tool_param_values:
+ value = tool_param_values[ name ]
+ if isinstance( value, DictifiableMixin ):
+ value = value.dictify()
+ t_input[ 'value' ] = value
+
+ return tool_dict
+
def get_visualization_config( self, trans, visualization ):
""" Returns a visualization's configuration. Only works for trackster visualizations right now. """
config = None
@@ -1137,7 +1177,7 @@
"prefs": prefs,
"mode": track_dict.get( 'mode', 'Auto' ),
"filters": track_dict.get( 'filters', { 'filters' : track_data_provider.get_filters() } ),
- "tool": get_tool_def( trans, dataset ),
+ "tool": self.get_tool_def( trans, dataset ),
"tool_state": track_dict.get( 'tool_state', {} )
}
@@ -1215,7 +1255,7 @@
"dataset": trans.security.encode_dict_ids( dataset.dictify() ),
"prefs": {},
"filters": { 'filters' : track_data_provider.get_filters() },
- "tool": get_tool_def( trans, dataset ),
+ "tool": self.get_tool_def( trans, dataset ),
"tool_state": {}
}
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/webapps/galaxy/api/datasets.py
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -199,7 +199,7 @@
data_dict = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom, low=low, high=high )
if data_dict:
ref_seq = data_dict[ 'data' ]
-
+
# Get and return data from data_provider.
result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ),
ref_seq=ref_seq, **kwargs )
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/webapps/galaxy/api/tools.py
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -1,6 +1,5 @@
from galaxy import web, util
from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin
-from galaxy.visualization.genome.visual_analytics import get_dataset_job
from galaxy.visualization.genomes import GenomeRegion
from galaxy.util.json import to_json_string, from_json_string
from galaxy.visualization.data_providers.genome import *
@@ -33,7 +32,7 @@
# Create return value.
try:
- return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster )
+ return self.app.toolbox.dictify( trans, in_panel=in_panel, trackster=trackster )
except Exception, exc:
log.error( 'could not convert toolbox to dictionary: %s', str( exc ), exc_info=True )
trans.response.status = 500
@@ -46,7 +45,7 @@
Returns tool information, including parameters and inputs.
"""
try:
- return self.app.toolbox.tools_by_id[ id ].to_dict( trans, for_display=True )
+ return self.app.toolbox.tools_by_id[ id ].dictify( trans, for_display=True )
except Exception, exc:
log.error( 'could not convert tool (%s) to dictionary: %s', id, str( exc ), exc_info=True )
trans.response.status = 500
@@ -217,7 +216,7 @@
# job's previous parameters and incoming parameters. Incoming parameters
# have priority.
#
- original_job = get_dataset_job( original_dataset )
+ original_job = self.get_hda_job( original_dataset )
tool = trans.app.toolbox.get_tool( original_job.tool_id )
if not tool:
return trans.app.model.Dataset.conversion_messages.NO_TOOL
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 lib/galaxy/webapps/galaxy/controllers/visualization.py
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -14,7 +14,6 @@
from galaxy.util.json import from_json_string
from galaxy.util.sanitize_html import sanitize_html
from galaxy.visualization.genomes import decode_dbkey
-from galaxy.visualization.genome.visual_analytics import get_dataset_job
from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
from galaxy.visualization.genomes import GenomeRegion
@@ -865,7 +864,7 @@
else:
# Loading new visualization.
dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
- job = get_dataset_job( dataset )
+ job = self.get_hda_job( dataset )
viz_config = {
'dataset_id': dataset_id,
'tool_id': job.tool_id,
@@ -874,7 +873,7 @@
# Add tool, dataset attributes to config based on id.
tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] )
- viz_config[ 'tool' ] = tool.to_dict( trans, for_display=True )
+ viz_config[ 'tool' ] = tool.dictify( trans, for_display=True )
viz_config[ 'dataset' ] = dataset.dictify()
return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config )
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -268,12 +268,12 @@
/**
* Label or section header in tool panel.
*/
-var ToolPanelLabel = Backbone.Model.extend(VisibilityMixin);
+var ToolSectionLabel = Backbone.Model.extend(VisibilityMixin);
/**
* Section of tool panel with elements (labels and tools).
*/
-var ToolPanelSection = Backbone.Model.extend({
+var ToolSection = Backbone.Model.extend({
defaults: {
elems: [],
open: false
@@ -292,7 +292,7 @@
var all_hidden = true,
cur_label;
_.each(this.attributes.elems, function(elt) {
- if (elt instanceof ToolPanelLabel) {
+ if (elt instanceof ToolSectionLabel) {
cur_label = elt;
cur_label.hide();
}
@@ -315,7 +315,7 @@
}
}
});
-_.extend(ToolPanelSection.prototype, VisibilityMixin);
+_.extend(ToolSection.prototype, VisibilityMixin);
/**
* Tool search that updates results when query is changed. Result value of null
@@ -399,18 +399,20 @@
var self = this,
// Helper to recursively parse tool panel.
parse_elt = function(elt_dict) {
- var type = elt_dict.type;
- if (type === 'tool') {
+ var type = elt_dict.model_class;
+ // There are many types of tools; for now, anything that ends in 'Tool'
+ // is treated as a generic tool.
+ if ( type.indexOf('Tool') === type.length - 4 ) {
return self.attributes.tools.get(elt_dict.id);
}
- else if (type === 'section') {
+ else if (type === 'ToolSection') {
// Parse elements.
var elems = _.map(elt_dict.elems, parse_elt);
elt_dict.elems = elems;
- return new ToolPanelSection(elt_dict);
+ return new ToolSection(elt_dict);
}
- else if (type === 'label') {
- return new ToolPanelLabel(elt_dict);
+ else if (type === 'ToolSectionLabel') {
+ return new ToolSectionLabel(elt_dict);
}
};
@@ -419,7 +421,7 @@
clear_search_results: function() {
this.get('layout').each(function(panel_elt) {
- if (panel_elt instanceof ToolPanelSection) {
+ if (panel_elt instanceof ToolSection) {
panel_elt.clear_search_results();
}
else {
@@ -438,7 +440,7 @@
var cur_label = null;
this.get('layout').each(function(panel_elt) {
- if (panel_elt instanceof ToolPanelLabel) {
+ if (panel_elt instanceof ToolSectionLabel) {
cur_label = panel_elt;
cur_label.hide();
}
@@ -495,12 +497,12 @@
/**
* Panel label/section header.
*/
-var ToolPanelLabelView = BaseView.extend({
+var ToolSectionLabelView = BaseView.extend({
tagName: 'div',
- className: 'toolPanelLabel',
+ className: 'ToolSectionLabel',
render: function() {
- this.$el.append( $("<span/>").text(this.model.attributes.name) );
+ this.$el.append( $("<span/>").text(this.model.attributes.text) );
return this;
}
});
@@ -508,7 +510,7 @@
/**
* Panel section.
*/
-var ToolPanelSectionView = BaseView.extend({
+var ToolSectionView = BaseView.extend({
tagName: 'div',
className: 'toolSectionWrapper',
template: Handlebars.templates.panel_section,
@@ -528,8 +530,8 @@
tool_view.render();
section_body.append(tool_view.$el);
}
- else if (elt instanceof ToolPanelLabel) {
- var label_view = new ToolPanelLabelView({model: elt});
+ else if (elt instanceof ToolSectionLabel) {
+ var label_view = new ToolSectionLabelView({model: elt});
label_view.render();
section_body.append(label_view.$el);
}
@@ -630,8 +632,8 @@
// Render panel.
this.model.get('layout').each(function(panel_elt) {
- if (panel_elt instanceof ToolPanelSection) {
- var section_title_view = new ToolPanelSectionView({model: panel_elt});
+ if (panel_elt instanceof ToolSection) {
+ var section_title_view = new ToolSectionView({model: panel_elt});
section_title_view.render();
self.$el.append(section_title_view.$el);
}
@@ -640,8 +642,8 @@
tool_view.render();
self.$el.append(tool_view.$el);
}
- else if (panel_elt instanceof ToolPanelLabel) {
- var label_view = new ToolPanelLabelView({model: panel_elt});
+ else if (panel_elt instanceof ToolSectionLabel) {
+ var label_view = new ToolSectionLabelView({model: panel_elt});
label_view.render();
self.$el.append(label_view.$el);
}
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 static/scripts/packed/libs/jquery/jstorage.js
--- a/static/scripts/packed/libs/jquery/jstorage.js
+++ b/static/scripts/packed/libs/jquery/jstorage.js
@@ -1,1 +1,1 @@
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diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 static/scripts/packed/libs/require.js
--- a/static/scripts/packed/libs/require.js
+++ b/static/scripts/packed/libs/require.js
@@ -1,1 +1,1 @@
-var requirejs,require,define;(function(global){var req,s,head,baseElement,dataMain,src,interactiveScript,currentlyAddingScript,mainScript,subPath,version="2.0.6",commentRegExp=/(\/\*([\s\S]*?)\*\/|([^:]|^)\/\/(.*)$)/mg,cjsRequireRegExp=/[^.]\s*require\s*\(\s*["']([^'"\s]+)["']\s*\)/g,jsSuffixRegExp=/\.js$/,currDirRegExp=/^\.\//,op=Object.prototype,ostring=op.toString,hasOwn=op.hasOwnProperty,ap=Array.prototype,aps=ap.slice,apsp=ap.splice,isBrowser=!!(typeof window!=="undefined"&&navigator&&document),isWebWorker=!isBrowser&&typeof importScripts!=="undefined",readyRegExp=isBrowser&&navigator.platform==="PLAYSTATION 3"?/^complete$/:/^(complete|loaded)$/,defContextName="_",isOpera=typeof opera!=="undefined"&&opera.toString()==="[object Opera]",contexts={},cfg={},globalDefQueue=[],useInteractive=false;function isFunction(it){return ostring.call(it)==="[object Function]"}function isArray(it){return ostring.call(it)==="[object Array]"}function each(ary,func){if(ary){var i;for(i=0;i<ary.length;i+=1){if(ary[i]&&func(ary[i],i,ary)){break}}}}function eachReverse(ary,func){if(ary){var i;for(i=ary.length-1;i>-1;i-=1){if(ary[i]&&func(ary[i],i,ary)){break}}}}function hasProp(obj,prop){return hasOwn.call(obj,prop)}function eachProp(obj,func){var prop;for(prop in obj){if(obj.hasOwnProperty(prop)){if(func(obj[prop],prop)){break}}}}function mixin(target,source,force,deepStringMixin){if(source){eachProp(source,function(value,prop){if(force||!hasProp(target,prop)){if(deepStringMixin&&typeof value!=="string"){if(!target[prop]){target[prop]={}}mixin(target[prop],value,force,deepStringMixin)}else{target[prop]=value}}})}return target}function bind(obj,fn){return function(){return fn.apply(obj,arguments)}}function scripts(){return document.getElementsByTagName("script")}function getGlobal(value){if(!value){return value}var g=global;each(value.split("."),function(part){g=g[part]});return g}function makeContextModuleFunc(func,relMap,enableBuildCallback){return function(){var args=aps.call(arguments,0),lastArg;if(enableBuildCallback&&isFunction((lastArg=args[args.length-1]))){lastArg.__requireJsBuild=true}args.push(relMap);return func.apply(null,args)}}function addRequireMethods(req,context,relMap){each([["toUrl"],["undef"],["defined","requireDefined"],["specified","requireSpecified"]],function(item){var prop=item[1]||item[0];req[item[0]]=context?makeContextModuleFunc(context[prop],relMap):function(){var ctx=contexts[defContextName];return ctx[prop].apply(ctx,arguments)}})}function makeError(id,msg,err,requireModules){var e=new Error(msg+"\nhttp://requirejs.org/docs/errors.html#"+id);e.requireType=id;e.requireModules=requireModules;if(err){e.originalError=err}return e}if(typeof define!=="undefined"){return}if(typeof requirejs!=="undefined"){if(isFunction(requirejs)){return}cfg=requirejs;requirejs=undefined}if(typeof require!=="undefined"&&!isFunction(require)){cfg=require;require=undefined}function newContext(contextName){var inCheckLoaded,Module,context,handlers,checkLoadedTimeoutId,config={waitSeconds:7,baseUrl:"./",paths:{},pkgs:{},shim:{}},registry={},undefEvents={},defQueue=[],defined={},urlFetched={},requireCounter=1,unnormalizedCounter=1,waitAry=[];function trimDots(ary){var i,part;for(i=0;ary[i];i+=1){part=ary[i];if(part==="."){ary.splice(i,1);i-=1}else{if(part===".."){if(i===1&&(ary[2]===".."||ary[0]==="..")){break}else{if(i>0){ary.splice(i-1,2);i-=2}}}}}}function normalize(name,baseName,applyMap){var pkgName,pkgConfig,mapValue,nameParts,i,j,nameSegment,foundMap,foundI,foundStarMap,starI,baseParts=baseName&&baseName.split("/"),normalizedBaseParts=baseParts,map=config.map,starMap=map&&map["*"];if(name&&name.charAt(0)==="."){if(baseName){if(config.pkgs[baseName]){normalizedBaseParts=baseParts=[baseName]}else{normalizedBaseParts=baseParts.slice(0,baseParts.length-1)}name=normalizedBaseParts.concat(name.split("/"));trimDots(name);pkgConfig=config.pkgs[(pkgName=name[0])];name=name.join("/");if(pkgConfig&&name===pkgName+"/"+pkgConfig.main){name=pkgName}}else{if(name.indexOf("./")===0){name=name.substring(2)}}}if(applyMap&&(baseParts||starMap)&&map){nameParts=name.split("/");for(i=nameParts.length;i>0;i-=1){nameSegment=nameParts.slice(0,i).join("/");if(baseParts){for(j=baseParts.length;j>0;j-=1){mapValue=map[baseParts.slice(0,j).join("/")];if(mapValue){mapValue=mapValue[nameSegment];if(mapValue){foundMap=mapValue;foundI=i;break}}}}if(foundMap){break}if(!foundStarMap&&starMap&&starMap[nameSegment]){foundStarMap=starMap[nameSegment];starI=i}}if(!foundMap&&foundStarMap){foundMap=foundStarMap;foundI=starI}if(foundMap){nameParts.splice(0,foundI,foundMap);name=nameParts.join("/")}}return name}function removeScript(name){if(isBrowser){each(scripts(),function(scriptNode){if(scriptNode.getAttribute("data-requiremodule")===name&&scriptNode.getAttribute("data-requirecontext")===context.contextName){scriptNode.parentNode.removeChild(scriptNode);return true}})}}function hasPathFallback(id){var pathConfig=config.paths[id];if(pathConfig&&isArray(pathConfig)&&pathConfig.length>1){removeScript(id);pathConfig.shift();context.undef(id);context.require([id]);return true}}function makeModuleMap(name,parentModuleMap,isNormalized,applyMap){var url,pluginModule,suffix,index=name?name.indexOf("!"):-1,prefix=null,parentName=parentModuleMap?parentModuleMap.name:null,originalName=name,isDefine=true,normalizedName="";if(!name){isDefine=false;name="_@r"+(requireCounter+=1)}if(index!==-1){prefix=name.substring(0,index);name=name.substring(index+1,name.length)}if(prefix){prefix=normalize(prefix,parentName,applyMap);pluginModule=defined[prefix]}if(name){if(prefix){if(pluginModule&&pluginModule.normalize){normalizedName=pluginModule.normalize(name,function(name){return normalize(name,parentName,applyMap)})}else{normalizedName=normalize(name,parentName,applyMap)}}else{normalizedName=normalize(name,parentName,applyMap);url=context.nameToUrl(normalizedName)}}suffix=prefix&&!pluginModule&&!isNormalized?"_unnormalized"+(unnormalizedCounter+=1):"";return{prefix:prefix,name:normalizedName,parentMap:parentModuleMap,unnormalized:!!suffix,url:url,originalName:originalName,isDefine:isDefine,id:(prefix?prefix+"!"+normalizedName:normalizedName)+suffix}}function getModule(depMap){var id=depMap.id,mod=registry[id];if(!mod){mod=registry[id]=new context.Module(depMap)}return mod}function on(depMap,name,fn){var id=depMap.id,mod=registry[id];if(hasProp(defined,id)&&(!mod||mod.defineEmitComplete)){if(name==="defined"){fn(defined[id])}}else{getModule(depMap).on(name,fn)}}function onError(err,errback){var ids=err.requireModules,notified=false;if(errback){errback(err)}else{each(ids,function(id){var mod=registry[id];if(mod){mod.error=err;if(mod.events.error){notified=true;mod.emit("error",err)}}});if(!notified){req.onError(err)}}}function takeGlobalQueue(){if(globalDefQueue.length){apsp.apply(defQueue,[defQueue.length-1,0].concat(globalDefQueue));globalDefQueue=[]}}function makeRequire(mod,enableBuildCallback,altRequire){var relMap=mod&&mod.map,modRequire=makeContextModuleFunc(altRequire||context.require,relMap,enableBuildCallback);addRequireMethods(modRequire,context,relMap);modRequire.isBrowser=isBrowser;return modRequire}handlers={require:function(mod){return makeRequire(mod)},exports:function(mod){mod.usingExports=true;if(mod.map.isDefine){return(mod.exports=defined[mod.map.id]={})}},module:function(mod){return(mod.module={id:mod.map.id,uri:mod.map.url,config:function(){return(config.config&&config.config[mod.map.id])||{}},exports:defined[mod.map.id]})}};function removeWaiting(id){delete registry[id];each(waitAry,function(mod,i){if(mod.map.id===id){waitAry.splice(i,1);if(!mod.defined){context.waitCount-=1}return true}})}function findCycle(mod,traced,processed){var id=mod.map.id,depArray=mod.depMaps,foundModule;if(!mod.inited){return}if(traced[id]){return mod}traced[id]=true;each(depArray,function(depMap){var depId=depMap.id,depMod=registry[depId];if(!depMod||processed[depId]||!depMod.inited||!depMod.enabled){return}return(foundModule=findCycle(depMod,traced,processed))});processed[id]=true;return foundModule}function forceExec(mod,traced,uninited){var id=mod.map.id,depArray=mod.depMaps;if(!mod.inited||!mod.map.isDefine){return}if(traced[id]){return defined[id]}traced[id]=mod;each(depArray,function(depMap){var depId=depMap.id,depMod=registry[depId],value;if(handlers[depId]){return}if(depMod){if(!depMod.inited||!depMod.enabled){uninited[id]=true;return}value=forceExec(depMod,traced,uninited);if(!uninited[depId]){mod.defineDepById(depId,value)}}});mod.check(true);return defined[id]}function modCheck(mod){mod.check()}function checkLoaded(){var map,modId,err,usingPathFallback,waitInterval=config.waitSeconds*1000,expired=waitInterval&&(context.startTime+waitInterval)<new Date().getTime(),noLoads=[],stillLoading=false,needCycleCheck=true;if(inCheckLoaded){return}inCheckLoaded=true;eachProp(registry,function(mod){map=mod.map;modId=map.id;if(!mod.enabled){return}if(!mod.error){if(!mod.inited&&expired){if(hasPathFallback(modId)){usingPathFallback=true;stillLoading=true}else{noLoads.push(modId);removeScript(modId)}}else{if(!mod.inited&&mod.fetched&&map.isDefine){stillLoading=true;if(!map.prefix){return(needCycleCheck=false)}}}}});if(expired&&noLoads.length){err=makeError("timeout","Load timeout for modules: "+noLoads,null,noLoads);err.contextName=context.contextName;return onError(err)}if(needCycleCheck){each(waitAry,function(mod){if(mod.defined){return}var cycleMod=findCycle(mod,{},{}),traced={};if(cycleMod){forceExec(cycleMod,traced,{});eachProp(traced,modCheck)}});eachProp(registry,modCheck)}if((!expired||usingPathFallback)&&stillLoading){if((isBrowser||isWebWorker)&&!checkLoadedTimeoutId){checkLoadedTimeoutId=setTimeout(function(){checkLoadedTimeoutId=0;checkLoaded()},50)}}inCheckLoaded=false}Module=function(map){this.events=undefEvents[map.id]||{};this.map=map;this.shim=config.shim[map.id];this.depExports=[];this.depMaps=[];this.depMatched=[];this.pluginMaps={};this.depCount=0};Module.prototype={init:function(depMaps,factory,errback,options){options=options||{};if(this.inited){return}this.factory=factory;if(errback){this.on("error",errback)}else{if(this.events.error){errback=bind(this,function(err){this.emit("error",err)})}}this.depMaps=depMaps&&depMaps.slice(0);this.depMaps.rjsSkipMap=depMaps.rjsSkipMap;this.errback=errback;this.inited=true;this.ignore=options.ignore;if(options.enabled||this.enabled){this.enable()}else{this.check()}},defineDepById:function(id,depExports){var i;each(this.depMaps,function(map,index){if(map.id===id){i=index;return true}});return this.defineDep(i,depExports)},defineDep:function(i,depExports){if(!this.depMatched[i]){this.depMatched[i]=true;this.depCount-=1;this.depExports[i]=depExports}},fetch:function(){if(this.fetched){return}this.fetched=true;context.startTime=(new Date()).getTime();var map=this.map;if(this.shim){makeRequire(this,true)(this.shim.deps||[],bind(this,function(){return map.prefix?this.callPlugin():this.load()}))}else{return map.prefix?this.callPlugin():this.load()}},load:function(){var url=this.map.url;if(!urlFetched[url]){urlFetched[url]=true;context.load(this.map.id,url)}},check:function(silent){if(!this.enabled||this.enabling){return}var err,cjsModule,id=this.map.id,depExports=this.depExports,exports=this.exports,factory=this.factory;if(!this.inited){this.fetch()}else{if(this.error){this.emit("error",this.error)}else{if(!this.defining){this.defining=true;if(this.depCount<1&&!this.defined){if(isFunction(factory)){if(this.events.error){try{exports=context.execCb(id,factory,depExports,exports)}catch(e){err=e}}else{exports=context.execCb(id,factory,depExports,exports)}if(this.map.isDefine){cjsModule=this.module;if(cjsModule&&cjsModule.exports!==undefined&&cjsModule.exports!==this.exports){exports=cjsModule.exports}else{if(exports===undefined&&this.usingExports){exports=this.exports}}}if(err){err.requireMap=this.map;err.requireModules=[this.map.id];err.requireType="define";return onError((this.error=err))}}else{exports=factory}this.exports=exports;if(this.map.isDefine&&!this.ignore){defined[id]=exports;if(req.onResourceLoad){req.onResourceLoad(context,this.map,this.depMaps)}}delete registry[id];this.defined=true;context.waitCount-=1;if(context.waitCount===0){waitAry=[]}}this.defining=false;if(!silent){if(this.defined&&!this.defineEmitted){this.defineEmitted=true;this.emit("defined",this.exports);this.defineEmitComplete=true}}}}}},callPlugin:function(){var map=this.map,id=map.id,pluginMap=makeModuleMap(map.prefix,null,false,true);on(pluginMap,"defined",bind(this,function(plugin){var load,normalizedMap,normalizedMod,name=this.map.name,parentName=this.map.parentMap?this.map.parentMap.name:null;if(this.map.unnormalized){if(plugin.normalize){name=plugin.normalize(name,function(name){return normalize(name,parentName,true)})||""}normalizedMap=makeModuleMap(map.prefix+"!"+name,this.map.parentMap,false,true);on(normalizedMap,"defined",bind(this,function(value){this.init([],function(){return value},null,{enabled:true,ignore:true})}));normalizedMod=registry[normalizedMap.id];if(normalizedMod){if(this.events.error){normalizedMod.on("error",bind(this,function(err){this.emit("error",err)}))}normalizedMod.enable()}return}load=bind(this,function(value){this.init([],function(){return value},null,{enabled:true})});load.error=bind(this,function(err){this.inited=true;this.error=err;err.requireModules=[id];eachProp(registry,function(mod){if(mod.map.id.indexOf(id+"_unnormalized")===0){removeWaiting(mod.map.id)}});onError(err)});load.fromText=function(moduleName,text){var hasInteractive=useInteractive;if(hasInteractive){useInteractive=false}getModule(makeModuleMap(moduleName));req.exec(text);if(hasInteractive){useInteractive=true}context.completeLoad(moduleName)};plugin.load(map.name,makeRequire(map.parentMap,true,function(deps,cb,er){deps.rjsSkipMap=true;return context.require(deps,cb,er)}),load,config)}));context.enable(pluginMap,this);this.pluginMaps[pluginMap.id]=pluginMap},enable:function(){this.enabled=true;if(!this.waitPushed){waitAry.push(this);context.waitCount+=1;this.waitPushed=true}this.enabling=true;each(this.depMaps,bind(this,function(depMap,i){var id,mod,handler;if(typeof depMap==="string"){depMap=makeModuleMap(depMap,(this.map.isDefine?this.map:this.map.parentMap),false,!this.depMaps.rjsSkipMap);this.depMaps[i]=depMap;handler=handlers[depMap.id];if(handler){this.depExports[i]=handler(this);return}this.depCount+=1;on(depMap,"defined",bind(this,function(depExports){this.defineDep(i,depExports);this.check()}));if(this.errback){on(depMap,"error",this.errback)}}id=depMap.id;mod=registry[id];if(!handlers[id]&&mod&&!mod.enabled){context.enable(depMap,this)}}));eachProp(this.pluginMaps,bind(this,function(pluginMap){var mod=registry[pluginMap.id];if(mod&&!mod.enabled){context.enable(pluginMap,this)}}));this.enabling=false;this.check()},on:function(name,cb){var cbs=this.events[name];if(!cbs){cbs=this.events[name]=[]}cbs.push(cb)},emit:function(name,evt){each(this.events[name],function(cb){cb(evt)});if(name==="error"){delete this.events[name]}}};function callGetModule(args){getModule(makeModuleMap(args[0],null,true)).init(args[1],args[2])}function removeListener(node,func,name,ieName){if(node.detachEvent&&!isOpera){if(ieName){node.detachEvent(ieName,func)}}else{node.removeEventListener(name,func,false)}}function getScriptData(evt){var node=evt.currentTarget||evt.srcElement;removeListener(node,context.onScriptLoad,"load","onreadystatechange");removeListener(node,context.onScriptError,"error");return{node:node,id:node&&node.getAttribute("data-requiremodule")}}return(context={config:config,contextName:contextName,registry:registry,defined:defined,urlFetched:urlFetched,waitCount:0,defQueue:defQueue,Module:Module,makeModuleMap:makeModuleMap,configure:function(cfg){if(cfg.baseUrl){if(cfg.baseUrl.charAt(cfg.baseUrl.length-1)!=="/"){cfg.baseUrl+="/"}}var pkgs=config.pkgs,shim=config.shim,paths=config.paths,map=config.map;mixin(config,cfg,true);config.paths=mixin(paths,cfg.paths,true);if(cfg.map){config.map=mixin(map||{},cfg.map,true,true)}if(cfg.shim){eachProp(cfg.shim,function(value,id){if(isArray(value)){value={deps:value}}if(value.exports&&!value.exports.__buildReady){value.exports=context.makeShimExports(value.exports)}shim[id]=value});config.shim=shim}if(cfg.packages){each(cfg.packages,function(pkgObj){var location;pkgObj=typeof pkgObj==="string"?{name:pkgObj}:pkgObj;location=pkgObj.location;pkgs[pkgObj.name]={name:pkgObj.name,location:location||pkgObj.name,main:(pkgObj.main||"main").replace(currDirRegExp,"").replace(jsSuffixRegExp,"")}});config.pkgs=pkgs}eachProp(registry,function(mod,id){if(!mod.inited&&!mod.map.unnormalized){mod.map=makeModuleMap(id)}});if(cfg.deps||cfg.callback){context.require(cfg.deps||[],cfg.callback)}},makeShimExports:function(exports){var func;if(typeof exports==="string"){func=function(){return getGlobal(exports)};func.exports=exports;return func}else{return function(){return exports.apply(global,arguments)}}},requireDefined:function(id,relMap){return hasProp(defined,makeModuleMap(id,relMap,false,true).id)},requireSpecified:function(id,relMap){id=makeModuleMap(id,relMap,false,true).id;return hasProp(defined,id)||hasProp(registry,id)},require:function(deps,callback,errback,relMap){var moduleName,id,map,requireMod,args;if(typeof deps==="string"){if(isFunction(callback)){return onError(makeError("requireargs","Invalid require call"),errback)}if(req.get){return req.get(context,deps,callback)}moduleName=deps;relMap=callback;map=makeModuleMap(moduleName,relMap,false,true);id=map.id;if(!hasProp(defined,id)){return onError(makeError("notloaded",'Module name "'+id+'" has not been loaded yet for context: '+contextName))}return defined[id]}if(errback&&!isFunction(errback)){relMap=errback;errback=undefined}if(callback&&!isFunction(callback)){relMap=callback;callback=undefined}takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){return onError(makeError("mismatch","Mismatched anonymous define() module: "+args[args.length-1]))}else{callGetModule(args)}}requireMod=getModule(makeModuleMap(null,relMap));requireMod.init(deps,callback,errback,{enabled:true});checkLoaded();return context.require},undef:function(id){takeGlobalQueue();var map=makeModuleMap(id,null,true),mod=registry[id];delete defined[id];delete urlFetched[map.url];delete undefEvents[id];if(mod){if(mod.events.defined){undefEvents[id]=mod.events}removeWaiting(id)}},enable:function(depMap,parent){var mod=registry[depMap.id];if(mod){getModule(depMap).enable()}},completeLoad:function(moduleName){var found,args,mod,shim=config.shim[moduleName]||{},shExports=shim.exports&&shim.exports.exports;takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){args[0]=moduleName;if(found){break}found=true}else{if(args[0]===moduleName){found=true}}callGetModule(args)}mod=registry[moduleName];if(!found&&!defined[moduleName]&&mod&&!mod.inited){if(config.enforceDefine&&(!shExports||!getGlobal(shExports))){if(hasPathFallback(moduleName)){return}else{return onError(makeError("nodefine","No define call for "+moduleName,null,[moduleName]))}}else{callGetModule([moduleName,(shim.deps||[]),shim.exports])}}checkLoaded()},toUrl:function(moduleNamePlusExt,relModuleMap){var index=moduleNamePlusExt.lastIndexOf("."),ext=null;if(index!==-1){ext=moduleNamePlusExt.substring(index,moduleNamePlusExt.length);moduleNamePlusExt=moduleNamePlusExt.substring(0,index)}return context.nameToUrl(normalize(moduleNamePlusExt,relModuleMap&&relModuleMap.id,true),ext)},nameToUrl:function(moduleName,ext){var paths,pkgs,pkg,pkgPath,syms,i,parentModule,url,parentPath;if(req.jsExtRegExp.test(moduleName)){url=moduleName+(ext||"")}else{paths=config.paths;pkgs=config.pkgs;syms=moduleName.split("/");for(i=syms.length;i>0;i-=1){parentModule=syms.slice(0,i).join("/");pkg=pkgs[parentModule];parentPath=paths[parentModule];if(parentPath){if(isArray(parentPath)){parentPath=parentPath[0]}syms.splice(0,i,parentPath);break}else{if(pkg){if(moduleName===pkg.name){pkgPath=pkg.location+"/"+pkg.main}else{pkgPath=pkg.location}syms.splice(0,i,pkgPath);break}}}url=syms.join("/");url+=(ext||(/\?/.test(url)?"":".js"));url=(url.charAt(0)==="/"||url.match(/^[\w\+\.\-]+:/)?"":config.baseUrl)+url}return config.urlArgs?url+((url.indexOf("?")===-1?"?":"&")+config.urlArgs):url},load:function(id,url){req.load(context,id,url)},execCb:function(name,callback,args,exports){return callback.apply(exports,args)},onScriptLoad:function(evt){if(evt.type==="load"||(readyRegExp.test((evt.currentTarget||evt.srcElement).readyState))){interactiveScript=null;var data=getScriptData(evt);context.completeLoad(data.id)}},onScriptError:function(evt){var data=getScriptData(evt);if(!hasPathFallback(data.id)){return onError(makeError("scripterror","Script error",evt,[data.id]))}}})}req=requirejs=function(deps,callback,errback,optional){var context,config,contextName=defContextName;if(!isArray(deps)&&typeof deps!=="string"){config=deps;if(isArray(callback)){deps=callback;callback=errback;errback=optional}else{deps=[]}}if(config&&config.context){contextName=config.context}context=contexts[contextName];if(!context){context=contexts[contextName]=req.s.newContext(contextName)}if(config){context.configure(config)}return context.require(deps,callback,errback)};req.config=function(config){return req(config)};if(!require){require=req}req.version=version;req.jsExtRegExp=/^\/|:|\?|\.js$/;req.isBrowser=isBrowser;s=req.s={contexts:contexts,newContext:newContext};req({});addRequireMethods(req);if(isBrowser){head=s.head=document.getElementsByTagName("head")[0];baseElement=document.getElementsByTagName("base")[0];if(baseElement){head=s.head=baseElement.parentNode}}req.onError=function(err){throw err};req.load=function(context,moduleName,url){var config=(context&&context.config)||{},node;if(isBrowser){node=config.xhtml?document.createElementNS("http://www.w3.org/1999/xhtml","html:script"):document.createElement("script");node.type=config.scriptType||"text/javascript";node.charset="utf-8";node.async=true;node.setAttribute("data-requirecontext",context.contextName);node.setAttribute("data-requiremodule",moduleName);if(node.attachEvent&&!(node.attachEvent.toString&&node.attachEvent.toString().indexOf("[native code")<0)&&!isOpera){useInteractive=true;node.attachEvent("onreadystatechange",context.onScriptLoad)}else{node.addEventListener("load",context.onScriptLoad,false);node.addEventListener("error",context.onScriptError,false)}node.src=url;currentlyAddingScript=node;if(baseElement){head.insertBefore(node,baseElement)}else{head.appendChild(node)}currentlyAddingScript=null;return node}else{if(isWebWorker){importScripts(url);context.completeLoad(moduleName)}}};function getInteractiveScript(){if(interactiveScript&&interactiveScript.readyState==="interactive"){return interactiveScript}eachReverse(scripts(),function(script){if(script.readyState==="interactive"){return(interactiveScript=script)}});return interactiveScript}if(isBrowser){eachReverse(scripts(),function(script){if(!head){head=script.parentNode}dataMain=script.getAttribute("data-main");if(dataMain){if(!cfg.baseUrl){src=dataMain.split("/");mainScript=src.pop();subPath=src.length?src.join("/")+"/":"./";cfg.baseUrl=subPath;dataMain=mainScript}dataMain=dataMain.replace(jsSuffixRegExp,"");cfg.deps=cfg.deps?cfg.deps.concat(dataMain):[dataMain];return true}})}define=function(name,deps,callback){var node,context;if(typeof name!=="string"){callback=deps;deps=name;name=null}if(!isArray(deps)){callback=deps;deps=[]}if(!deps.length&&isFunction(callback)){if(callback.length){callback.toString().replace(commentRegExp,"").replace(cjsRequireRegExp,function(match,dep){deps.push(dep)});deps=(callback.length===1?["require"]:["require","exports","module"]).concat(deps)}}if(useInteractive){node=currentlyAddingScript||getInteractiveScript();if(node){if(!name){name=node.getAttribute("data-requiremodule")}context=contexts[node.getAttribute("data-requirecontext")]}}(context?context.defQueue:globalDefQueue).push([name,deps,callback])};define.amd={jQuery:true};req.exec=function(text){return eval(text)};req(cfg)}(this));
\ No newline at end of file
+var requirejs,require,define;(function(global){var req,s,head,baseElement,dataMain,src,interactiveScript,currentlyAddingScript,mainScript,subPath,version="2.1.8",commentRegExp=/(\/\*([\s\S]*?)\*\/|([^:]|^)\/\/(.*)$)/mg,cjsRequireRegExp=/[^.]\s*require\s*\(\s*["']([^'"\s]+)["']\s*\)/g,jsSuffixRegExp=/\.js$/,currDirRegExp=/^\.\//,op=Object.prototype,ostring=op.toString,hasOwn=op.hasOwnProperty,ap=Array.prototype,apsp=ap.splice,isBrowser=!!(typeof window!=="undefined"&&navigator&&window.document),isWebWorker=!isBrowser&&typeof importScripts!=="undefined",readyRegExp=isBrowser&&navigator.platform==="PLAYSTATION 3"?/^complete$/:/^(complete|loaded)$/,defContextName="_",isOpera=typeof opera!=="undefined"&&opera.toString()==="[object Opera]",contexts={},cfg={},globalDefQueue=[],useInteractive=false;function isFunction(it){return ostring.call(it)==="[object Function]"}function isArray(it){return ostring.call(it)==="[object Array]"}function each(ary,func){if(ary){var i;for(i=0;i<ary.length;i+=1){if(ary[i]&&func(ary[i],i,ary)){break}}}}function eachReverse(ary,func){if(ary){var i;for(i=ary.length-1;i>-1;i-=1){if(ary[i]&&func(ary[i],i,ary)){break}}}}function hasProp(obj,prop){return hasOwn.call(obj,prop)}function getOwn(obj,prop){return hasProp(obj,prop)&&obj[prop]}function eachProp(obj,func){var prop;for(prop in obj){if(hasProp(obj,prop)){if(func(obj[prop],prop)){break}}}}function mixin(target,source,force,deepStringMixin){if(source){eachProp(source,function(value,prop){if(force||!hasProp(target,prop)){if(deepStringMixin&&typeof value!=="string"){if(!target[prop]){target[prop]={}}mixin(target[prop],value,force,deepStringMixin)}else{target[prop]=value}}})}return target}function bind(obj,fn){return function(){return fn.apply(obj,arguments)}}function scripts(){return document.getElementsByTagName("script")}function defaultOnError(err){throw err}function getGlobal(value){if(!value){return value}var g=global;each(value.split("."),function(part){g=g[part]});return g}function makeError(id,msg,err,requireModules){var e=new Error(msg+"\nhttp://requirejs.org/docs/errors.html#"+id);e.requireType=id;e.requireModules=requireModules;if(err){e.originalError=err}return e}if(typeof define!=="undefined"){return}if(typeof requirejs!=="undefined"){if(isFunction(requirejs)){return}cfg=requirejs;requirejs=undefined}if(typeof require!=="undefined"&&!isFunction(require)){cfg=require;require=undefined}function newContext(contextName){var inCheckLoaded,Module,context,handlers,checkLoadedTimeoutId,config={waitSeconds:7,baseUrl:"./",paths:{},pkgs:{},shim:{},config:{}},registry={},enabledRegistry={},undefEvents={},defQueue=[],defined={},urlFetched={},requireCounter=1,unnormalizedCounter=1;function trimDots(ary){var i,part;for(i=0;ary[i];i+=1){part=ary[i];if(part==="."){ary.splice(i,1);i-=1}else{if(part===".."){if(i===1&&(ary[2]===".."||ary[0]==="..")){break}else{if(i>0){ary.splice(i-1,2);i-=2}}}}}}function normalize(name,baseName,applyMap){var pkgName,pkgConfig,mapValue,nameParts,i,j,nameSegment,foundMap,foundI,foundStarMap,starI,baseParts=baseName&&baseName.split("/"),normalizedBaseParts=baseParts,map=config.map,starMap=map&&map["*"];if(name&&name.charAt(0)==="."){if(baseName){if(getOwn(config.pkgs,baseName)){normalizedBaseParts=baseParts=[baseName]}else{normalizedBaseParts=baseParts.slice(0,baseParts.length-1)}name=normalizedBaseParts.concat(name.split("/"));trimDots(name);pkgConfig=getOwn(config.pkgs,(pkgName=name[0]));name=name.join("/");if(pkgConfig&&name===pkgName+"/"+pkgConfig.main){name=pkgName}}else{if(name.indexOf("./")===0){name=name.substring(2)}}}if(applyMap&&map&&(baseParts||starMap)){nameParts=name.split("/");for(i=nameParts.length;i>0;i-=1){nameSegment=nameParts.slice(0,i).join("/");if(baseParts){for(j=baseParts.length;j>0;j-=1){mapValue=getOwn(map,baseParts.slice(0,j).join("/"));if(mapValue){mapValue=getOwn(mapValue,nameSegment);if(mapValue){foundMap=mapValue;foundI=i;break}}}}if(foundMap){break}if(!foundStarMap&&starMap&&getOwn(starMap,nameSegment)){foundStarMap=getOwn(starMap,nameSegment);starI=i}}if(!foundMap&&foundStarMap){foundMap=foundStarMap;foundI=starI}if(foundMap){nameParts.splice(0,foundI,foundMap);name=nameParts.join("/")}}return name}function removeScript(name){if(isBrowser){each(scripts(),function(scriptNode){if(scriptNode.getAttribute("data-requiremodule")===name&&scriptNode.getAttribute("data-requirecontext")===context.contextName){scriptNode.parentNode.removeChild(scriptNode);return true}})}}function hasPathFallback(id){var pathConfig=getOwn(config.paths,id);if(pathConfig&&isArray(pathConfig)&&pathConfig.length>1){removeScript(id);pathConfig.shift();context.require.undef(id);context.require([id]);return true}}function splitPrefix(name){var prefix,index=name?name.indexOf("!"):-1;if(index>-1){prefix=name.substring(0,index);name=name.substring(index+1,name.length)}return[prefix,name]}function makeModuleMap(name,parentModuleMap,isNormalized,applyMap){var url,pluginModule,suffix,nameParts,prefix=null,parentName=parentModuleMap?parentModuleMap.name:null,originalName=name,isDefine=true,normalizedName="";if(!name){isDefine=false;name="_@r"+(requireCounter+=1)}nameParts=splitPrefix(name);prefix=nameParts[0];name=nameParts[1];if(prefix){prefix=normalize(prefix,parentName,applyMap);pluginModule=getOwn(defined,prefix)}if(name){if(prefix){if(pluginModule&&pluginModule.normalize){normalizedName=pluginModule.normalize(name,function(name){return normalize(name,parentName,applyMap)})}else{normalizedName=normalize(name,parentName,applyMap)}}else{normalizedName=normalize(name,parentName,applyMap);nameParts=splitPrefix(normalizedName);prefix=nameParts[0];normalizedName=nameParts[1];isNormalized=true;url=context.nameToUrl(normalizedName)}}suffix=prefix&&!pluginModule&&!isNormalized?"_unnormalized"+(unnormalizedCounter+=1):"";return{prefix:prefix,name:normalizedName,parentMap:parentModuleMap,unnormalized:!!suffix,url:url,originalName:originalName,isDefine:isDefine,id:(prefix?prefix+"!"+normalizedName:normalizedName)+suffix}}function getModule(depMap){var id=depMap.id,mod=getOwn(registry,id);if(!mod){mod=registry[id]=new context.Module(depMap)}return mod}function on(depMap,name,fn){var id=depMap.id,mod=getOwn(registry,id);if(hasProp(defined,id)&&(!mod||mod.defineEmitComplete)){if(name==="defined"){fn(defined[id])}}else{mod=getModule(depMap);if(mod.error&&name==="error"){fn(mod.error)}else{mod.on(name,fn)}}}function onError(err,errback){var ids=err.requireModules,notified=false;if(errback){errback(err)}else{each(ids,function(id){var mod=getOwn(registry,id);if(mod){mod.error=err;if(mod.events.error){notified=true;mod.emit("error",err)}}});if(!notified){req.onError(err)}}}function takeGlobalQueue(){if(globalDefQueue.length){apsp.apply(defQueue,[defQueue.length-1,0].concat(globalDefQueue));globalDefQueue=[]}}handlers={require:function(mod){if(mod.require){return mod.require}else{return(mod.require=context.makeRequire(mod.map))}},exports:function(mod){mod.usingExports=true;if(mod.map.isDefine){if(mod.exports){return mod.exports}else{return(mod.exports=defined[mod.map.id]={})}}},module:function(mod){if(mod.module){return mod.module}else{return(mod.module={id:mod.map.id,uri:mod.map.url,config:function(){var c,pkg=getOwn(config.pkgs,mod.map.id);c=pkg?getOwn(config.config,mod.map.id+"/"+pkg.main):getOwn(config.config,mod.map.id);return c||{}},exports:defined[mod.map.id]})}}};function cleanRegistry(id){delete registry[id];delete enabledRegistry[id]}function breakCycle(mod,traced,processed){var id=mod.map.id;if(mod.error){mod.emit("error",mod.error)}else{traced[id]=true;each(mod.depMaps,function(depMap,i){var depId=depMap.id,dep=getOwn(registry,depId);if(dep&&!mod.depMatched[i]&&!processed[depId]){if(getOwn(traced,depId)){mod.defineDep(i,defined[depId]);mod.check()}else{breakCycle(dep,traced,processed)}}});processed[id]=true}}function checkLoaded(){var map,modId,err,usingPathFallback,waitInterval=config.waitSeconds*1000,expired=waitInterval&&(context.startTime+waitInterval)<new Date().getTime(),noLoads=[],reqCalls=[],stillLoading=false,needCycleCheck=true;if(inCheckLoaded){return}inCheckLoaded=true;eachProp(enabledRegistry,function(mod){map=mod.map;modId=map.id;if(!mod.enabled){return}if(!map.isDefine){reqCalls.push(mod)}if(!mod.error){if(!mod.inited&&expired){if(hasPathFallback(modId)){usingPathFallback=true;stillLoading=true}else{noLoads.push(modId);removeScript(modId)}}else{if(!mod.inited&&mod.fetched&&map.isDefine){stillLoading=true;if(!map.prefix){return(needCycleCheck=false)}}}}});if(expired&&noLoads.length){err=makeError("timeout","Load timeout for modules: "+noLoads,null,noLoads);err.contextName=context.contextName;return onError(err)}if(needCycleCheck){each(reqCalls,function(mod){breakCycle(mod,{},{})})}if((!expired||usingPathFallback)&&stillLoading){if((isBrowser||isWebWorker)&&!checkLoadedTimeoutId){checkLoadedTimeoutId=setTimeout(function(){checkLoadedTimeoutId=0;checkLoaded()},50)}}inCheckLoaded=false}Module=function(map){this.events=getOwn(undefEvents,map.id)||{};this.map=map;this.shim=getOwn(config.shim,map.id);this.depExports=[];this.depMaps=[];this.depMatched=[];this.pluginMaps={};this.depCount=0};Module.prototype={init:function(depMaps,factory,errback,options){options=options||{};if(this.inited){return}this.factory=factory;if(errback){this.on("error",errback)}else{if(this.events.error){errback=bind(this,function(err){this.emit("error",err)})}}this.depMaps=depMaps&&depMaps.slice(0);this.errback=errback;this.inited=true;this.ignore=options.ignore;if(options.enabled||this.enabled){this.enable()}else{this.check()}},defineDep:function(i,depExports){if(!this.depMatched[i]){this.depMatched[i]=true;this.depCount-=1;this.depExports[i]=depExports}},fetch:function(){if(this.fetched){return}this.fetched=true;context.startTime=(new Date()).getTime();var map=this.map;if(this.shim){context.makeRequire(this.map,{enableBuildCallback:true})(this.shim.deps||[],bind(this,function(){return map.prefix?this.callPlugin():this.load()}))}else{return map.prefix?this.callPlugin():this.load()}},load:function(){var url=this.map.url;if(!urlFetched[url]){urlFetched[url]=true;context.load(this.map.id,url)}},check:function(){if(!this.enabled||this.enabling){return}var err,cjsModule,id=this.map.id,depExports=this.depExports,exports=this.exports,factory=this.factory;if(!this.inited){this.fetch()}else{if(this.error){this.emit("error",this.error)}else{if(!this.defining){this.defining=true;if(this.depCount<1&&!this.defined){if(isFunction(factory)){if((this.events.error&&this.map.isDefine)||req.onError!==defaultOnError){try{exports=context.execCb(id,factory,depExports,exports)}catch(e){err=e}}else{exports=context.execCb(id,factory,depExports,exports)}if(this.map.isDefine){cjsModule=this.module;if(cjsModule&&cjsModule.exports!==undefined&&cjsModule.exports!==this.exports){exports=cjsModule.exports}else{if(exports===undefined&&this.usingExports){exports=this.exports}}}if(err){err.requireMap=this.map;err.requireModules=this.map.isDefine?[this.map.id]:null;err.requireType=this.map.isDefine?"define":"require";return onError((this.error=err))}}else{exports=factory}this.exports=exports;if(this.map.isDefine&&!this.ignore){defined[id]=exports;if(req.onResourceLoad){req.onResourceLoad(context,this.map,this.depMaps)}}cleanRegistry(id);this.defined=true}this.defining=false;if(this.defined&&!this.defineEmitted){this.defineEmitted=true;this.emit("defined",this.exports);this.defineEmitComplete=true}}}}},callPlugin:function(){var map=this.map,id=map.id,pluginMap=makeModuleMap(map.prefix);this.depMaps.push(pluginMap);on(pluginMap,"defined",bind(this,function(plugin){var load,normalizedMap,normalizedMod,name=this.map.name,parentName=this.map.parentMap?this.map.parentMap.name:null,localRequire=context.makeRequire(map.parentMap,{enableBuildCallback:true});if(this.map.unnormalized){if(plugin.normalize){name=plugin.normalize(name,function(name){return 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moduleName=map.name,moduleMap=makeModuleMap(moduleName),hasInteractive=useInteractive;if(textAlt){text=textAlt}if(hasInteractive){useInteractive=false}getModule(moduleMap);if(hasProp(config.config,id)){config.config[moduleName]=config.config[id]}try{req.exec(text)}catch(e){return onError(makeError("fromtexteval","fromText eval for "+id+" failed: "+e,e,[id]))}if(hasInteractive){useInteractive=true}this.depMaps.push(moduleMap);context.completeLoad(moduleName);localRequire([moduleName],load)});plugin.load(map.name,localRequire,load,config)}));context.enable(pluginMap,this);this.pluginMaps[pluginMap.id]=pluginMap},enable:function(){enabledRegistry[this.map.id]=this;this.enabled=true;this.enabling=true;each(this.depMaps,bind(this,function(depMap,i){var id,mod,handler;if(typeof depMap==="string"){depMap=makeModuleMap(depMap,(this.map.isDefine?this.map:this.map.parentMap),false,!this.skipMap);this.depMaps[i]=depMap;handler=getOwn(handlers,depMap.id);if(handler){this.depExports[i]=handler(this);return}this.depCount+=1;on(depMap,"defined",bind(this,function(depExports){this.defineDep(i,depExports);this.check()}));if(this.errback){on(depMap,"error",bind(this,this.errback))}}id=depMap.id;mod=registry[id];if(!hasProp(handlers,id)&&mod&&!mod.enabled){context.enable(depMap,this)}}));eachProp(this.pluginMaps,bind(this,function(pluginMap){var mod=getOwn(registry,pluginMap.id);if(mod&&!mod.enabled){context.enable(pluginMap,this)}}));this.enabling=false;this.check()},on:function(name,cb){var cbs=this.events[name];if(!cbs){cbs=this.events[name]=[]}cbs.push(cb)},emit:function(name,evt){each(this.events[name],function(cb){cb(evt)});if(name==="error"){delete this.events[name]}}};function callGetModule(args){if(!hasProp(defined,args[0])){getModule(makeModuleMap(args[0],null,true)).init(args[1],args[2])}}function removeListener(node,func,name,ieName){if(node.detachEvent&&!isOpera){if(ieName){node.detachEvent(ieName,func)}}else{node.removeEventListener(name,func,false)}}function getScriptData(evt){var node=evt.currentTarget||evt.srcElement;removeListener(node,context.onScriptLoad,"load","onreadystatechange");removeListener(node,context.onScriptError,"error");return{node:node,id:node&&node.getAttribute("data-requiremodule")}}function intakeDefines(){var args;takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){return onError(makeError("mismatch","Mismatched anonymous define() module: "+args[args.length-1]))}else{callGetModule(args)}}}context={config:config,contextName:contextName,registry:registry,defined:defined,urlFetched:urlFetched,defQueue:defQueue,Module:Module,makeModuleMap:makeModuleMap,nextTick:req.nextTick,onError:onError,configure:function(cfg){if(cfg.baseUrl){if(cfg.baseUrl.charAt(cfg.baseUrl.length-1)!=="/"){cfg.baseUrl+="/"}}var pkgs=config.pkgs,shim=config.shim,objs={paths:true,config:true,map:true};eachProp(cfg,function(value,prop){if(objs[prop]){if(prop==="map"){if(!config.map){config.map={}}mixin(config[prop],value,true,true)}else{mixin(config[prop],value,true)}}else{config[prop]=value}});if(cfg.shim){eachProp(cfg.shim,function(value,id){if(isArray(value)){value={deps:value}}if((value.exports||value.init)&&!value.exportsFn){value.exportsFn=context.makeShimExports(value)}shim[id]=value});config.shim=shim}if(cfg.packages){each(cfg.packages,function(pkgObj){var location;pkgObj=typeof pkgObj==="string"?{name:pkgObj}:pkgObj;location=pkgObj.location;pkgs[pkgObj.name]={name:pkgObj.name,location:location||pkgObj.name,main:(pkgObj.main||"main").replace(currDirRegExp,"").replace(jsSuffixRegExp,"")}});config.pkgs=pkgs}eachProp(registry,function(mod,id){if(!mod.inited&&!mod.map.unnormalized){mod.map=makeModuleMap(id)}});if(cfg.deps||cfg.callback){context.require(cfg.deps||[],cfg.callback)}},makeShimExports:function(value){function fn(){var ret;if(value.init){ret=value.init.apply(global,arguments)}return ret||(value.exports&&getGlobal(value.exports))}return fn},makeRequire:function(relMap,options){options=options||{};function localRequire(deps,callback,errback){var id,map,requireMod;if(options.enableBuildCallback&&callback&&isFunction(callback)){callback.__requireJsBuild=true}if(typeof deps==="string"){if(isFunction(callback)){return onError(makeError("requireargs","Invalid require call"),errback)}if(relMap&&hasProp(handlers,deps)){return handlers[deps](registry[relMap.id])}if(req.get){return req.get(context,deps,relMap,localRequire)}map=makeModuleMap(deps,relMap,false,true);id=map.id;if(!hasProp(defined,id)){return onError(makeError("notloaded",'Module name "'+id+'" has not been loaded yet for context: '+contextName+(relMap?"":". Use require([])")))}return defined[id]}intakeDefines();context.nextTick(function(){intakeDefines();requireMod=getModule(makeModuleMap(null,relMap));requireMod.skipMap=options.skipMap;requireMod.init(deps,callback,errback,{enabled:true});checkLoaded()});return localRequire}mixin(localRequire,{isBrowser:isBrowser,toUrl:function(moduleNamePlusExt){var ext,index=moduleNamePlusExt.lastIndexOf("."),segment=moduleNamePlusExt.split("/")[0],isRelative=segment==="."||segment==="..";if(index!==-1&&(!isRelative||index>1)){ext=moduleNamePlusExt.substring(index,moduleNamePlusExt.length);moduleNamePlusExt=moduleNamePlusExt.substring(0,index)}return context.nameToUrl(normalize(moduleNamePlusExt,relMap&&relMap.id,true),ext,true)},defined:function(id){return hasProp(defined,makeModuleMap(id,relMap,false,true).id)},specified:function(id){id=makeModuleMap(id,relMap,false,true).id;return hasProp(defined,id)||hasProp(registry,id)}});if(!relMap){localRequire.undef=function(id){takeGlobalQueue();var map=makeModuleMap(id,relMap,true),mod=getOwn(registry,id);delete defined[id];delete urlFetched[map.url];delete undefEvents[id];if(mod){if(mod.events.defined){undefEvents[id]=mod.events}cleanRegistry(id)}}}return localRequire},enable:function(depMap){var mod=getOwn(registry,depMap.id);if(mod){getModule(depMap).enable()}},completeLoad:function(moduleName){var found,args,mod,shim=getOwn(config.shim,moduleName)||{},shExports=shim.exports;takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){args[0]=moduleName;if(found){break}found=true}else{if(args[0]===moduleName){found=true}}callGetModule(args)}mod=getOwn(registry,moduleName);if(!found&&!hasProp(defined,moduleName)&&mod&&!mod.inited){if(config.enforceDefine&&(!shExports||!getGlobal(shExports))){if(hasPathFallback(moduleName)){return}else{return onError(makeError("nodefine","No define call for "+moduleName,null,[moduleName]))}}else{callGetModule([moduleName,(shim.deps||[]),shim.exportsFn])}}checkLoaded()},nameToUrl:function(moduleName,ext,skipExt){var paths,pkgs,pkg,pkgPath,syms,i,parentModule,url,parentPath;if(req.jsExtRegExp.test(moduleName)){url=moduleName+(ext||"")}else{paths=config.paths;pkgs=config.pkgs;syms=moduleName.split("/");for(i=syms.length;i>0;i-=1){parentModule=syms.slice(0,i).join("/");pkg=getOwn(pkgs,parentModule);parentPath=getOwn(paths,parentModule);if(parentPath){if(isArray(parentPath)){parentPath=parentPath[0]}syms.splice(0,i,parentPath);break}else{if(pkg){if(moduleName===pkg.name){pkgPath=pkg.location+"/"+pkg.main}else{pkgPath=pkg.location}syms.splice(0,i,pkgPath);break}}}url=syms.join("/");url+=(ext||(/\?/.test(url)||skipExt?"":".js"));url=(url.charAt(0)==="/"||url.match(/^[\w\+\.\-]+:/)?"":config.baseUrl)+url}return config.urlArgs?url+((url.indexOf("?")===-1?"?":"&")+config.urlArgs):url},load:function(id,url){req.load(context,id,url)},execCb:function(name,callback,args,exports){return callback.apply(exports,args)},onScriptLoad:function(evt){if(evt.type==="load"||(readyRegExp.test((evt.currentTarget||evt.srcElement).readyState))){interactiveScript=null;var data=getScriptData(evt);context.completeLoad(data.id)}},onScriptError:function(evt){var data=getScriptData(evt);if(!hasPathFallback(data.id)){return onError(makeError("scripterror","Script error for: "+data.id,evt,[data.id]))}}};context.require=context.makeRequire();return context}req=requirejs=function(deps,callback,errback,optional){var context,config,contextName=defContextName;if(!isArray(deps)&&typeof deps!=="string"){config=deps;if(isArray(callback)){deps=callback;callback=errback;errback=optional}else{deps=[]}}if(config&&config.context){contextName=config.context}context=getOwn(contexts,contextName);if(!context){context=contexts[contextName]=req.s.newContext(contextName)}if(config){context.configure(config)}return context.require(deps,callback,errback)};req.config=function(config){return req(config)};req.nextTick=typeof setTimeout!=="undefined"?function(fn){setTimeout(fn,4)}:function(fn){fn()};if(!require){require=req}req.version=version;req.jsExtRegExp=/^\/|:|\?|\.js$/;req.isBrowser=isBrowser;s=req.s={contexts:contexts,newContext:newContext};req({});each(["toUrl","undef","defined","specified"],function(prop){req[prop]=function(){var ctx=contexts[defContextName];return ctx.require[prop].apply(ctx,arguments)}});if(isBrowser){head=s.head=document.getElementsByTagName("head")[0];baseElement=document.getElementsByTagName("base")[0];if(baseElement){head=s.head=baseElement.parentNode}}req.onError=defaultOnError;req.createNode=function(config,moduleName,url){var node=config.xhtml?document.createElementNS("http://www.w3.org/1999/xhtml","html:script"):document.createElement("script");node.type=config.scriptType||"text/javascript";node.charset="utf-8";node.async=true;return node};req.load=function(context,moduleName,url){var config=(context&&context.config)||{},node;if(isBrowser){node=req.createNode(config,moduleName,url);node.setAttribute("data-requirecontext",context.contextName);node.setAttribute("data-requiremodule",moduleName);if(node.attachEvent&&!(node.attachEvent.toString&&node.attachEvent.toString().indexOf("[native code")<0)&&!isOpera){useInteractive=true;node.attachEvent("onreadystatechange",context.onScriptLoad)}else{node.addEventListener("load",context.onScriptLoad,false);node.addEventListener("error",context.onScriptError,false)}node.src=url;currentlyAddingScript=node;if(baseElement){head.insertBefore(node,baseElement)}else{head.appendChild(node)}currentlyAddingScript=null;return node}else{if(isWebWorker){try{importScripts(url);context.completeLoad(moduleName)}catch(e){context.onError(makeError("importscripts","importScripts failed for "+moduleName+" at "+url,e,[moduleName]))}}}};function getInteractiveScript(){if(interactiveScript&&interactiveScript.readyState==="interactive"){return interactiveScript}eachReverse(scripts(),function(script){if(script.readyState==="interactive"){return(interactiveScript=script)}});return interactiveScript}if(isBrowser){eachReverse(scripts(),function(script){if(!head){head=script.parentNode}dataMain=script.getAttribute("data-main");if(dataMain){mainScript=dataMain;if(!cfg.baseUrl){src=mainScript.split("/");mainScript=src.pop();subPath=src.length?src.join("/")+"/":"./";cfg.baseUrl=subPath}mainScript=mainScript.replace(jsSuffixRegExp,"");if(req.jsExtRegExp.test(mainScript)){mainScript=dataMain}cfg.deps=cfg.deps?cfg.deps.concat(mainScript):[mainScript];return true}})}define=function(name,deps,callback){var node,context;if(typeof name!=="string"){callback=deps;deps=name;name=null}if(!isArray(deps)){callback=deps;deps=null}if(!deps&&isFunction(callback)){deps=[];if(callback.length){callback.toString().replace(commentRegExp,"").replace(cjsRequireRegExp,function(match,dep){deps.push(dep)});deps=(callback.length===1?["require"]:["require","exports","module"]).concat(deps)}}if(useInteractive){node=currentlyAddingScript||getInteractiveScript();if(node){if(!name){name=node.getAttribute("data-requiremodule")}context=contexts[node.getAttribute("data-requirecontext")]}}(context?context.defQueue:globalDefQueue).push([name,deps,callback])};define.amd={jQuery:true};req.exec=function(text){return eval(text)};req(cfg)}(this));
\ No newline at end of file
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 static/scripts/packed/mvc/tools.js
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var e={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var d=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new d(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:c},create:function(v){var w=d.TYPE_DICT[v.type]||d;return new w(v)}});var c=d.extend({defaults:t.extend({},d.prototype.defaults,{min:null,max:null}),initialize:function(){d.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return d.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,e);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var o=Backbone.Model.extend(e);var r=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof o){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(r.prototype,e);var b=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(b.prototype,e);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.type;if(z==="tool"){return v.attributes.tools.get(A.id)}else{if(z==="section"){var y=t.map(A.elems,x);A.elems=y;return new r(A)}else{if(z==="label"){return new o(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof r){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof o){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var f=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var i=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof o){var y=new f({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof r){var x=new i({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof o){var A=new f({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:d,IntegerToolParameter:c,Tool:h,ToolCollection:k,ToolSearch:b,ToolPanel:l,ToolPanelView:s,ToolFormView:q}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var f={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:d},create:function(v){var w=e.TYPE_DICT[v.type]||e;return new w(v)}});var d=e.extend({defaults:t.extend({},e.prototype.defaults,{min:null,max:null}),initialize:function(){e.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return e.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,f);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var r=Backbone.Model.extend(f);var i=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof r){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(i.prototype,f);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(c.prototype,f);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.model_class;if(z.indexOf("Tool")===z.length-4){return v.attributes.tools.get(A.id)}else{if(z==="ToolSection"){var y=t.map(A.elems,x);A.elems=y;return new i(A)}else{if(z==="ToolSectionLabel"){return new r(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof i){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof r){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var b=p.extend({tagName:"div",className:"ToolSectionLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var o=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof r){var y=new b({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof i){var x=new o({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof r){var A=new b({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,Tool:h,ToolCollection:k,ToolSearch:c,ToolPanel:l,ToolPanelView:s,ToolFormView:q}});
\ No newline at end of file
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 static/scripts/packed/viz/trackster/tracks.js
--- a/static/scripts/packed/viz/trackster/tracks.js
+++ b/static/scripts/packed/viz/trackster/tracks.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}]});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}],initialize:function(ae){var ad=this.get("tool"),af=ad.get("inputs").filter(function(ag){return(["data","hidden_data","group"].indexOf(ag.get("type"))!==-1)});ad.get("inputs").remove(af)}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1634,7 +1634,17 @@
key: 'tool',
relatedModel: tools_mod.Tool
}
- ]
+ ],
+
+ initialize: function(options) {
+ // HACK: remove data and group tool inputs because Trackster
+ // does not work with them right now.
+ var tool = this.get('tool'),
+ incompatible_inputs = tool.get('inputs').filter( function(input) {
+ return ( [ 'data', 'hidden_data', 'group'].indexOf( input.get('type') ) !== -1);
+ });
+ tool.get('inputs').remove(incompatible_inputs);
+ }
});
@@ -1692,6 +1702,7 @@
// Add name, inputs.
var name_div = $("<div class='tool-name'>").appendTo(parent_div).text(tool.get('name'));
tool.get('inputs').each(function(param) {
+ // Render parameter.
var param_view = new ToolParameterView({ model: param });
param_view.render();
parent_div.append(param_view.$el);
@@ -2479,11 +2490,8 @@
Drawable.prototype.action_icons_def[2]
],
- can_draw: function() {
- if ( this.dataset.id && Drawable.prototype.can_draw.call(this) ) {
- return true;
- }
- return false;
+ can_draw: function() {
+ return this.dataset && Drawable.prototype.can_draw.call(this);
},
build_container_div: function () {
diff -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 templates/webapps/galaxy/root/tool_menu.mako
--- a/templates/webapps/galaxy/root/tool_menu.mako
+++ b/templates/webapps/galaxy/root/tool_menu.mako
@@ -25,12 +25,12 @@
hidden: false
}),
tools = new tools_mod.ToolCollection(
- ${ h.to_json_string( trans.app.toolbox.to_dict( trans, in_panel=False ) ) }
+ ${ h.to_json_string( trans.app.toolbox.dictify( trans, in_panel=False ) ) }
),
tool_panel = new tools_mod.ToolPanel({
tool_search: tool_search,
tools: tools,
- layout: ${h.to_json_string( trans.app.toolbox.to_dict( trans ) )}
+ layout: ${h.to_json_string( trans.app.toolbox.dictify( trans ) )}
}),
tool_panel_view = new tools_mod.ToolPanelView({ model: tool_panel });
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Functional tests: fix sqlite db_path var; fix api test for hda update with nonsense key
by commits-noreplyï¼ bitbucket.org 22 Aug '13
by commits-noreplyï¼ bitbucket.org 22 Aug '13
22 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/33092bc258d7/
Changeset: 33092bc258d7
User: carlfeberhard
Date: 2013-08-21 19:00:09
Summary: Functional tests: fix sqlite db_path var; fix api test for hda update with nonsense key
Affected #: 2 files
diff -r 408f39acefc287815aa0c2672cc92f0f83e55ff9 -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 scripts/functional_tests.py
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -243,7 +243,7 @@
if 'GALAXY_TEST_DBURI' in os.environ:
database_connection = os.environ['GALAXY_TEST_DBURI']
else:
- database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' )
+ database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'universe.sqlite' )
kwargs = {}
for dir in file_path, new_file_path:
try:
diff -r 408f39acefc287815aa0c2672cc92f0f83e55ff9 -r 33092bc258d7b11668bfe9ea0d5b6e3817ac0a46 test/casperjs/api-hda-tests.js
--- a/test/casperjs/api-hda-tests.js
+++ b/test/casperjs/api-hda-tests.js
@@ -135,18 +135,11 @@
});
this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) );
- this.test.comment( 'updating using a nonsense key should fail with an error' );
- var err = {};
- try {
- returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
- konamiCode : 'uuddlrlrba'
- });
- } catch( error ){
- err = error;
- //this.debug( this.jsonStr( err ) );
- }
- this.test.assert( !!err.message, "Error occurred: " + err.message );
- this.test.assert( err.status === 400, "Error status is 400: " + err.status );
+ this.test.comment( 'updating using a nonsense key should NOT fail with an error' );
+ returned = this.api.hdas.update( lastHistory.id, firstHda.id, {
+ konamiCode : 'uuddlrlrba'
+ });
+ this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) );
this.test.comment( 'updating by attempting to change type should cause an error' );
err = {};
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Update require.js to 2.1.8
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/408f39acefc2/
Changeset: 408f39acefc2
User: guerler
Date: 2013-08-21 18:29:37
Summary: Update require.js to 2.1.8
Affected #: 1 file
diff -r 8ab88925e5eff54a056722bdf0fb3622d0a0455c -r 408f39acefc287815aa0c2672cc92f0f83e55ff9 static/scripts/libs/require.js
--- a/static/scripts/libs/require.js
+++ b/static/scripts/libs/require.js
@@ -1,18 +1,18 @@
/** vim: et:ts=4:sw=4:sts=4
- * @license RequireJS 2.0.6 Copyright (c) 2010-2012, The Dojo Foundation All Rights Reserved.
+ * @license RequireJS 2.1.8 Copyright (c) 2010-2012, The Dojo Foundation All Rights Reserved.
* Available via the MIT or new BSD license.
* see: http://github.com/jrburke/requirejs for details
*/
//Not using strict: uneven strict support in browsers, #392, and causes
//problems with requirejs.exec()/transpiler plugins that may not be strict.
/*jslint regexp: true, nomen: true, sloppy: true */
-/*global window, navigator, document, importScripts, jQuery, setTimeout, opera */
+/*global window, navigator, document, importScripts, setTimeout, opera */
var requirejs, require, define;
(function (global) {
var req, s, head, baseElement, dataMain, src,
interactiveScript, currentlyAddingScript, mainScript, subPath,
- version = '2.0.6',
+ version = '2.1.8',
commentRegExp = /(\/\*([\s\S]*?)\*\/|([^:]|^)\/\/(.*)$)/mg,
cjsRequireRegExp = /[^.]\s*require\s*\(\s*["']([^'"\s]+)["']\s*\)/g,
jsSuffixRegExp = /\.js$/,
@@ -21,9 +21,8 @@
ostring = op.toString,
hasOwn = op.hasOwnProperty,
ap = Array.prototype,
- aps = ap.slice,
apsp = ap.splice,
- isBrowser = !!(typeof window !== 'undefined' && navigator && document),
+ isBrowser = !!(typeof window !== 'undefined' && navigator && window.document),
isWebWorker = !isBrowser && typeof importScripts !== 'undefined',
//PS3 indicates loaded and complete, but need to wait for complete
//specifically. Sequence is 'loading', 'loaded', execution,
@@ -81,6 +80,10 @@
return hasOwn.call(obj, prop);
}
+ function getOwn(obj, prop) {
+ return hasProp(obj, prop) && obj[prop];
+ }
+
/**
* Cycles over properties in an object and calls a function for each
* property value. If the function returns a truthy value, then the
@@ -89,7 +92,7 @@
function eachProp(obj, func) {
var prop;
for (prop in obj) {
- if (obj.hasOwnProperty(prop)) {
+ if (hasProp(obj, prop)) {
if (func(obj[prop], prop)) {
break;
}
@@ -100,9 +103,6 @@
/**
* Simple function to mix in properties from source into target,
* but only if target does not already have a property of the same name.
- * This is not robust in IE for transferring methods that match
- * Object.prototype names, but the uses of mixin here seem unlikely to
- * trigger a problem related to that.
*/
function mixin(target, source, force, deepStringMixin) {
if (source) {
@@ -134,6 +134,10 @@
return document.getElementsByTagName('script');
}
+ function defaultOnError(err) {
+ throw err;
+ }
+
//Allow getting a global that expressed in
//dot notation, like 'a.b.c'.
function getGlobal(value) {
@@ -147,41 +151,6 @@
return g;
}
- function makeContextModuleFunc(func, relMap, enableBuildCallback) {
- return function () {
- //A version of a require function that passes a moduleName
- //value for items that may need to
- //look up paths relative to the moduleName
- var args = aps.call(arguments, 0), lastArg;
- if (enableBuildCallback &&
- isFunction((lastArg = args[args.length - 1]))) {
- lastArg.__requireJsBuild = true;
- }
- args.push(relMap);
- return func.apply(null, args);
- };
- }
-
- function addRequireMethods(req, context, relMap) {
- each([
- ['toUrl'],
- ['undef'],
- ['defined', 'requireDefined'],
- ['specified', 'requireSpecified']
- ], function (item) {
- var prop = item[1] || item[0];
- req[item[0]] = context ? makeContextModuleFunc(context[prop], relMap) :
- //If no context, then use default context. Reference from
- //contexts instead of early binding to default context, so
- //that during builds, the latest instance of the default
- //context with its config gets used.
- function () {
- var ctx = contexts[defContextName];
- return ctx[prop].apply(ctx, arguments);
- };
- });
- }
-
/**
* Constructs an error with a pointer to an URL with more information.
* @param {String} id the error ID that maps to an ID on a web page.
@@ -226,24 +195,27 @@
var inCheckLoaded, Module, context, handlers,
checkLoadedTimeoutId,
config = {
+ //Defaults. Do not set a default for map
+ //config to speed up normalize(), which
+ //will run faster if there is no default.
waitSeconds: 7,
baseUrl: './',
paths: {},
pkgs: {},
- shim: {}
+ shim: {},
+ config: {}
},
registry = {},
+ //registry of just enabled modules, to speed
+ //cycle breaking code when lots of modules
+ //are registered, but not activated.
+ enabledRegistry = {},
undefEvents = {},
defQueue = [],
defined = {},
urlFetched = {},
requireCounter = 1,
- unnormalizedCounter = 1,
- //Used to track the order in which modules
- //should be executed, by the order they
- //load. Important for consistent cycle resolution
- //behavior.
- waitAry = [];
+ unnormalizedCounter = 1;
/**
* Trims the . and .. from an array of path segments.
@@ -302,7 +274,7 @@
//otherwise, assume it is a top-level require that will
//be relative to baseUrl in the end.
if (baseName) {
- if (config.pkgs[baseName]) {
+ if (getOwn(config.pkgs, baseName)) {
//If the baseName is a package name, then just treat it as one
//name to concat the name with.
normalizedBaseParts = baseParts = [baseName];
@@ -320,7 +292,7 @@
//Some use of packages may use a . path to reference the
//'main' module name, so normalize for that.
- pkgConfig = config.pkgs[(pkgName = name[0])];
+ pkgConfig = getOwn(config.pkgs, (pkgName = name[0]));
name = name.join('/');
if (pkgConfig && name === pkgName + '/' + pkgConfig.main) {
name = pkgName;
@@ -333,7 +305,7 @@
}
//Apply map config if available.
- if (applyMap && (baseParts || starMap) && map) {
+ if (applyMap && map && (baseParts || starMap)) {
nameParts = name.split('/');
for (i = nameParts.length; i > 0; i -= 1) {
@@ -343,12 +315,12 @@
//Find the longest baseName segment match in the config.
//So, do joins on the biggest to smallest lengths of baseParts.
for (j = baseParts.length; j > 0; j -= 1) {
- mapValue = map[baseParts.slice(0, j).join('/')];
+ mapValue = getOwn(map, baseParts.slice(0, j).join('/'));
//baseName segment has config, find if it has one for
//this name.
if (mapValue) {
- mapValue = mapValue[nameSegment];
+ mapValue = getOwn(mapValue, nameSegment);
if (mapValue) {
//Match, update name to the new value.
foundMap = mapValue;
@@ -366,8 +338,8 @@
//Check for a star map match, but just hold on to it,
//if there is a shorter segment match later in a matching
//config, then favor over this star map.
- if (!foundStarMap && starMap && starMap[nameSegment]) {
- foundStarMap = starMap[nameSegment];
+ if (!foundStarMap && starMap && getOwn(starMap, nameSegment)) {
+ foundStarMap = getOwn(starMap, nameSegment);
starI = i;
}
}
@@ -399,18 +371,31 @@
}
function hasPathFallback(id) {
- var pathConfig = config.paths[id];
+ var pathConfig = getOwn(config.paths, id);
if (pathConfig && isArray(pathConfig) && pathConfig.length > 1) {
removeScript(id);
//Pop off the first array value, since it failed, and
//retry
pathConfig.shift();
- context.undef(id);
+ context.require.undef(id);
context.require([id]);
return true;
}
}
+ //Turns a plugin!resource to [plugin, resource]
+ //with the plugin being undefined if the name
+ //did not have a plugin prefix.
+ function splitPrefix(name) {
+ var prefix,
+ index = name ? name.indexOf('!') : -1;
+ if (index > -1) {
+ prefix = name.substring(0, index);
+ name = name.substring(index + 1, name.length);
+ }
+ return [prefix, name];
+ }
+
/**
* Creates a module mapping that includes plugin prefix, module
* name, and path. If parentModuleMap is provided it will
@@ -427,8 +412,7 @@
* @returns {Object}
*/
function makeModuleMap(name, parentModuleMap, isNormalized, applyMap) {
- var url, pluginModule, suffix,
- index = name ? name.indexOf('!') : -1,
+ var url, pluginModule, suffix, nameParts,
prefix = null,
parentName = parentModuleMap ? parentModuleMap.name : null,
originalName = name,
@@ -442,14 +426,13 @@
name = '_@r' + (requireCounter += 1);
}
- if (index !== -1) {
- prefix = name.substring(0, index);
- name = name.substring(index + 1, name.length);
- }
+ nameParts = splitPrefix(name);
+ prefix = nameParts[0];
+ name = nameParts[1];
if (prefix) {
prefix = normalize(prefix, parentName, applyMap);
- pluginModule = defined[prefix];
+ pluginModule = getOwn(defined, prefix);
}
//Account for relative paths if there is a base name.
@@ -466,6 +449,15 @@
} else {
//A regular module.
normalizedName = normalize(name, parentName, applyMap);
+
+ //Normalized name may be a plugin ID due to map config
+ //application in normalize. The map config values must
+ //already be normalized, so do not need to redo that part.
+ nameParts = splitPrefix(normalizedName);
+ prefix = nameParts[0];
+ normalizedName = nameParts[1];
+ isNormalized = true;
+
url = context.nameToUrl(normalizedName);
}
}
@@ -493,7 +485,7 @@
function getModule(depMap) {
var id = depMap.id,
- mod = registry[id];
+ mod = getOwn(registry, id);
if (!mod) {
mod = registry[id] = new context.Module(depMap);
@@ -504,7 +496,7 @@
function on(depMap, name, fn) {
var id = depMap.id,
- mod = registry[id];
+ mod = getOwn(registry, id);
if (hasProp(defined, id) &&
(!mod || mod.defineEmitComplete)) {
@@ -512,7 +504,12 @@
fn(defined[id]);
}
} else {
- getModule(depMap).on(name, fn);
+ mod = getModule(depMap);
+ if (mod.error && name === 'error') {
+ fn(mod.error);
+ } else {
+ mod.on(name, fn);
+ }
}
}
@@ -524,7 +521,7 @@
errback(err);
} else {
each(ids, function (id) {
- var mod = registry[id];
+ var mod = getOwn(registry, id);
if (mod) {
//Set error on module, so it skips timeout checks.
mod.error = err;
@@ -557,148 +554,78 @@
}
}
- /**
- * Helper function that creates a require function object to give to
- * modules that ask for it as a dependency. It needs to be specific
- * per module because of the implication of path mappings that may
- * need to be relative to the module name.
- */
- function makeRequire(mod, enableBuildCallback, altRequire) {
- var relMap = mod && mod.map,
- modRequire = makeContextModuleFunc(altRequire || context.require,
- relMap,
- enableBuildCallback);
-
- addRequireMethods(modRequire, context, relMap);
- modRequire.isBrowser = isBrowser;
-
- return modRequire;
- }
-
handlers = {
'require': function (mod) {
- return makeRequire(mod);
+ if (mod.require) {
+ return mod.require;
+ } else {
+ return (mod.require = context.makeRequire(mod.map));
+ }
},
'exports': function (mod) {
mod.usingExports = true;
if (mod.map.isDefine) {
- return (mod.exports = defined[mod.map.id] = {});
+ if (mod.exports) {
+ return mod.exports;
+ } else {
+ return (mod.exports = defined[mod.map.id] = {});
+ }
}
},
'module': function (mod) {
- return (mod.module = {
- id: mod.map.id,
- uri: mod.map.url,
- config: function () {
- return (config.config && config.config[mod.map.id]) || {};
- },
- exports: defined[mod.map.id]
- });
+ if (mod.module) {
+ return mod.module;
+ } else {
+ return (mod.module = {
+ id: mod.map.id,
+ uri: mod.map.url,
+ config: function () {
+ var c,
+ pkg = getOwn(config.pkgs, mod.map.id);
+ // For packages, only support config targeted
+ // at the main module.
+ c = pkg ? getOwn(config.config, mod.map.id + '/' + pkg.main) :
+ getOwn(config.config, mod.map.id);
+ return c || {};
+ },
+ exports: defined[mod.map.id]
+ });
+ }
}
};
- function removeWaiting(id) {
+ function cleanRegistry(id) {
//Clean up machinery used for waiting modules.
delete registry[id];
-
- each(waitAry, function (mod, i) {
- if (mod.map.id === id) {
- waitAry.splice(i, 1);
- if (!mod.defined) {
- context.waitCount -= 1;
- }
- return true;
- }
- });
+ delete enabledRegistry[id];
}
- function findCycle(mod, traced, processed) {
- var id = mod.map.id,
- depArray = mod.depMaps,
- foundModule;
+ function breakCycle(mod, traced, processed) {
+ var id = mod.map.id;
- //Do not bother with unitialized modules or not yet enabled
- //modules.
- if (!mod.inited) {
- return;
+ if (mod.error) {
+ mod.emit('error', mod.error);
+ } else {
+ traced[id] = true;
+ each(mod.depMaps, function (depMap, i) {
+ var depId = depMap.id,
+ dep = getOwn(registry, depId);
+
+ //Only force things that have not completed
+ //being defined, so still in the registry,
+ //and only if it has not been matched up
+ //in the module already.
+ if (dep && !mod.depMatched[i] && !processed[depId]) {
+ if (getOwn(traced, depId)) {
+ mod.defineDep(i, defined[depId]);
+ mod.check(); //pass false?
+ } else {
+ breakCycle(dep, traced, processed);
+ }
+ }
+ });
+ processed[id] = true;
}
-
- //Found the cycle.
- if (traced[id]) {
- return mod;
- }
-
- traced[id] = true;
-
- //Trace through the dependencies.
- each(depArray, function (depMap) {
- var depId = depMap.id,
- depMod = registry[depId];
-
- if (!depMod || processed[depId] ||
- !depMod.inited || !depMod.enabled) {
- return;
- }
-
- return (foundModule = findCycle(depMod, traced, processed));
- });
-
- processed[id] = true;
-
- return foundModule;
- }
-
- function forceExec(mod, traced, uninited) {
- var id = mod.map.id,
- depArray = mod.depMaps;
-
- if (!mod.inited || !mod.map.isDefine) {
- return;
- }
-
- if (traced[id]) {
- return defined[id];
- }
-
- traced[id] = mod;
-
- each(depArray, function (depMap) {
- var depId = depMap.id,
- depMod = registry[depId],
- value;
-
- if (handlers[depId]) {
- return;
- }
-
- if (depMod) {
- if (!depMod.inited || !depMod.enabled) {
- //Dependency is not inited,
- //so this module cannot be
- //given a forced value yet.
- uninited[id] = true;
- return;
- }
-
- //Get the value for the current dependency
- value = forceExec(depMod, traced, uninited);
-
- //Even with forcing it may not be done,
- //in particular if the module is waiting
- //on a plugin resource.
- if (!uninited[depId]) {
- mod.defineDepById(depId, value);
- }
- }
- });
-
- mod.check(true);
-
- return defined[id];
- }
-
- function modCheck(mod) {
- mod.check();
}
function checkLoaded() {
@@ -707,6 +634,7 @@
//It is possible to disable the wait interval by using waitSeconds of 0.
expired = waitInterval && (context.startTime + waitInterval) < new Date().getTime(),
noLoads = [],
+ reqCalls = [],
stillLoading = false,
needCycleCheck = true;
@@ -718,7 +646,7 @@
inCheckLoaded = true;
//Figure out the state of all the modules.
- eachProp(registry, function (mod) {
+ eachProp(enabledRegistry, function (mod) {
map = mod.map;
modId = map.id;
@@ -727,6 +655,10 @@
return;
}
+ if (!map.isDefine) {
+ reqCalls.push(mod);
+ }
+
if (!mod.error) {
//If the module should be executed, and it has not
//been inited and time is up, remember it.
@@ -761,31 +693,9 @@
//Not expired, check for a cycle.
if (needCycleCheck) {
-
- each(waitAry, function (mod) {
- if (mod.defined) {
- return;
- }
-
- var cycleMod = findCycle(mod, {}, {}),
- traced = {};
-
- if (cycleMod) {
- forceExec(cycleMod, traced, {});
-
- //traced modules may have been
- //removed from the registry, but
- //their listeners still need to
- //be called.
- eachProp(traced, modCheck);
- }
+ each(reqCalls, function (mod) {
+ breakCycle(mod, {}, {});
});
-
- //Now that dependencies have
- //been satisfied, trigger the
- //completion check that then
- //notifies listeners.
- eachProp(registry, modCheck);
}
//If still waiting on loads, and the waiting load is something
@@ -806,9 +716,9 @@
}
Module = function (map) {
- this.events = undefEvents[map.id] || {};
+ this.events = getOwn(undefEvents, map.id) || {};
this.map = map;
- this.shim = config.shim[map.id];
+ this.shim = getOwn(config.shim, map.id);
this.depExports = [];
this.depMaps = [];
this.depMatched = [];
@@ -851,7 +761,6 @@
//doing a direct modification of the depMaps array
//would affect that config.
this.depMaps = depMaps && depMaps.slice(0);
- this.depMaps.rjsSkipMap = depMaps.rjsSkipMap;
this.errback = errback;
@@ -873,20 +782,6 @@
}
},
- defineDepById: function (id, depExports) {
- var i;
-
- //Find the index for this dependency.
- each(this.depMaps, function (map, index) {
- if (map.id === id) {
- i = index;
- return true;
- }
- });
-
- return this.defineDep(i, depExports);
- },
-
defineDep: function (i, depExports) {
//Because of cycles, defined callback for a given
//export can be called more than once.
@@ -910,7 +805,9 @@
//If the manager is for a plugin managed resource,
//ask the plugin to load it now.
if (this.shim) {
- makeRequire(this, true)(this.shim.deps || [], bind(this, function () {
+ context.makeRequire(this.map, {
+ enableBuildCallback: true
+ })(this.shim.deps || [], bind(this, function () {
return map.prefix ? this.callPlugin() : this.load();
}));
} else {
@@ -930,12 +827,10 @@
},
/**
- * Checks is the module is ready to define itself, and if so,
- * define it. If the silent argument is true, then it will just
- * define, but not notify listeners, and not ask for a context-wide
- * check of all loaded modules. That is useful for cycle breaking.
+ * Checks if the module is ready to define itself, and if so,
+ * define it.
*/
- check: function (silent) {
+ check: function () {
if (!this.enabled || this.enabling) {
return;
}
@@ -960,8 +855,13 @@
if (this.depCount < 1 && !this.defined) {
if (isFunction(factory)) {
//If there is an error listener, favor passing
- //to that instead of throwing an error.
- if (this.events.error) {
+ //to that instead of throwing an error. However,
+ //only do it for define()'d modules. require
+ //errbacks should not be called for failures in
+ //their callbacks (#699). However if a global
+ //onError is set, use that.
+ if ((this.events.error && this.map.isDefine) ||
+ req.onError !== defaultOnError) {
try {
exports = context.execCb(id, factory, depExports, exports);
} catch (e) {
@@ -989,8 +889,8 @@
if (err) {
err.requireMap = this.map;
- err.requireModules = [this.map.id];
- err.requireType = 'define';
+ err.requireModules = this.map.isDefine ? [this.map.id] : null;
+ err.requireType = this.map.isDefine ? 'define' : 'require';
return onError((this.error = err));
}
@@ -1010,14 +910,9 @@
}
//Clean up
- delete registry[id];
+ cleanRegistry(id);
this.defined = true;
- context.waitCount -= 1;
- if (context.waitCount === 0) {
- //Clear the wait array used for cycles.
- waitAry = [];
- }
}
//Finished the define stage. Allow calling check again
@@ -1025,25 +920,32 @@
//cycle.
this.defining = false;
- if (!silent) {
- if (this.defined && !this.defineEmitted) {
- this.defineEmitted = true;
- this.emit('defined', this.exports);
- this.defineEmitComplete = true;
- }
+ if (this.defined && !this.defineEmitted) {
+ this.defineEmitted = true;
+ this.emit('defined', this.exports);
+ this.defineEmitComplete = true;
}
+
}
},
callPlugin: function () {
var map = this.map,
id = map.id,
- pluginMap = makeModuleMap(map.prefix, null, false, true);
+ //Map already normalized the prefix.
+ pluginMap = makeModuleMap(map.prefix);
+
+ //Mark this as a dependency for this plugin, so it
+ //can be traced for cycles.
+ this.depMaps.push(pluginMap);
on(pluginMap, 'defined', bind(this, function (plugin) {
var load, normalizedMap, normalizedMod,
name = this.map.name,
- parentName = this.map.parentMap ? this.map.parentMap.name : null;
+ parentName = this.map.parentMap ? this.map.parentMap.name : null,
+ localRequire = context.makeRequire(map.parentMap, {
+ enableBuildCallback: true
+ });
//If current map is not normalized, wait for that
//normalized name to load instead of continuing.
@@ -1055,10 +957,10 @@
}) || '';
}
+ //prefix and name should already be normalized, no need
+ //for applying map config again either.
normalizedMap = makeModuleMap(map.prefix + '!' + name,
- this.map.parentMap,
- false,
- true);
+ this.map.parentMap);
on(normalizedMap,
'defined', bind(this, function (value) {
this.init([], function () { return value; }, null, {
@@ -1066,8 +968,13 @@
ignore: true
});
}));
- normalizedMod = registry[normalizedMap.id];
+
+ normalizedMod = getOwn(registry, normalizedMap.id);
if (normalizedMod) {
+ //Mark this as a dependency for this plugin, so it
+ //can be traced for cycles.
+ this.depMaps.push(normalizedMap);
+
if (this.events.error) {
normalizedMod.on('error', bind(this, function (err) {
this.emit('error', err);
@@ -1094,7 +1001,7 @@
//since they will never be resolved otherwise now.
eachProp(registry, function (mod) {
if (mod.map.id.indexOf(id + '_unnormalized') === 0) {
- removeWaiting(mod.map.id);
+ cleanRegistry(mod.map.id);
}
});
@@ -1103,9 +1010,19 @@
//Allow plugins to load other code without having to know the
//context or how to 'complete' the load.
- load.fromText = function (moduleName, text) {
+ load.fromText = bind(this, function (text, textAlt) {
/*jslint evil: true */
- var hasInteractive = useInteractive;
+ var moduleName = map.name,
+ moduleMap = makeModuleMap(moduleName),
+ hasInteractive = useInteractive;
+
+ //As of 2.1.0, support just passing the text, to reinforce
+ //fromText only being called once per resource. Still
+ //support old style of passing moduleName but discard
+ //that moduleName in favor of the internal ref.
+ if (textAlt) {
+ text = textAlt;
+ }
//Turn off interactive script matching for IE for any define
//calls in the text, then turn it back on at the end.
@@ -1115,25 +1032,43 @@
//Prime the system by creating a module instance for
//it.
- getModule(makeModuleMap(moduleName));
+ getModule(moduleMap);
- req.exec(text);
+ //Transfer any config to this other module.
+ if (hasProp(config.config, id)) {
+ config.config[moduleName] = config.config[id];
+ }
+
+ try {
+ req.exec(text);
+ } catch (e) {
+ return onError(makeError('fromtexteval',
+ 'fromText eval for ' + id +
+ ' failed: ' + e,
+ e,
+ [id]));
+ }
if (hasInteractive) {
useInteractive = true;
}
+ //Mark this as a dependency for the plugin
+ //resource
+ this.depMaps.push(moduleMap);
+
//Support anonymous modules.
context.completeLoad(moduleName);
- };
+
+ //Bind the value of that module to the value for this
+ //resource ID.
+ localRequire([moduleName], load);
+ });
//Use parentName here since the plugin's name is not reliable,
//could be some weird string with no path that actually wants to
//reference the parentName's path.
- plugin.load(map.name, makeRequire(map.parentMap, true, function (deps, cb, er) {
- deps.rjsSkipMap = true;
- return context.require(deps, cb, er);
- }), load, config);
+ plugin.load(map.name, localRequire, load, config);
}));
context.enable(pluginMap, this);
@@ -1141,14 +1076,9 @@
},
enable: function () {
+ enabledRegistry[this.map.id] = this;
this.enabled = true;
- if (!this.waitPushed) {
- waitAry.push(this);
- context.waitCount += 1;
- this.waitPushed = true;
- }
-
//Set flag mentioning that the module is enabling,
//so that immediate calls to the defined callbacks
//for dependencies do not trigger inadvertent load
@@ -1165,10 +1095,10 @@
depMap = makeModuleMap(depMap,
(this.map.isDefine ? this.map : this.map.parentMap),
false,
- !this.depMaps.rjsSkipMap);
+ !this.skipMap);
this.depMaps[i] = depMap;
- handler = handlers[depMap.id];
+ handler = getOwn(handlers, depMap.id);
if (handler) {
this.depExports[i] = handler(this);
@@ -1183,7 +1113,7 @@
}));
if (this.errback) {
- on(depMap, 'error', this.errback);
+ on(depMap, 'error', bind(this, this.errback));
}
}
@@ -1193,7 +1123,7 @@
//Skip special modules like 'require', 'exports', 'module'
//Also, don't call enable if it is already enabled,
//important in circular dependency cases.
- if (!handlers[id] && mod && !mod.enabled) {
+ if (!hasProp(handlers, id) && mod && !mod.enabled) {
context.enable(depMap, this);
}
}));
@@ -1201,7 +1131,7 @@
//Enable each plugin that is used in
//a dependency
eachProp(this.pluginMaps, bind(this, function (pluginMap) {
- var mod = registry[pluginMap.id];
+ var mod = getOwn(registry, pluginMap.id);
if (mod && !mod.enabled) {
context.enable(pluginMap, this);
}
@@ -1227,14 +1157,17 @@
if (name === 'error') {
//Now that the error handler was triggered, remove
//the listeners, since this broken Module instance
- //can stay around for a while in the registry/waitAry.
+ //can stay around for a while in the registry.
delete this.events[name];
}
}
};
function callGetModule(args) {
- getModule(makeModuleMap(args[0], null, true)).init(args[1], args[2]);
+ //Skip modules already defined.
+ if (!hasProp(defined, args[0])) {
+ getModule(makeModuleMap(args[0], null, true)).init(args[1], args[2]);
+ }
}
function removeListener(node, func, name, ieName) {
@@ -1274,16 +1207,36 @@
};
}
- return (context = {
+ function intakeDefines() {
+ var args;
+
+ //Any defined modules in the global queue, intake them now.
+ takeGlobalQueue();
+
+ //Make sure any remaining defQueue items get properly processed.
+ while (defQueue.length) {
+ args = defQueue.shift();
+ if (args[0] === null) {
+ return onError(makeError('mismatch', 'Mismatched anonymous define() module: ' + args[args.length - 1]));
+ } else {
+ //args are id, deps, factory. Should be normalized by the
+ //define() function.
+ callGetModule(args);
+ }
+ }
+ }
+
+ context = {
config: config,
contextName: contextName,
registry: registry,
defined: defined,
urlFetched: urlFetched,
- waitCount: 0,
defQueue: defQueue,
Module: Module,
makeModuleMap: makeModuleMap,
+ nextTick: req.nextTick,
+ onError: onError,
/**
* Set a configuration for the context.
@@ -1301,20 +1254,26 @@
//they are additive.
var pkgs = config.pkgs,
shim = config.shim,
- paths = config.paths,
- map = config.map;
+ objs = {
+ paths: true,
+ config: true,
+ map: true
+ };
- //Mix in the config values, favoring the new values over
- //existing ones in context.config.
- mixin(config, cfg, true);
-
- //Merge paths.
- config.paths = mixin(paths, cfg.paths, true);
-
- //Merge map
- if (cfg.map) {
- config.map = mixin(map || {}, cfg.map, true, true);
- }
+ eachProp(cfg, function (value, prop) {
+ if (objs[prop]) {
+ if (prop === 'map') {
+ if (!config.map) {
+ config.map = {};
+ }
+ mixin(config[prop], value, true, true);
+ } else {
+ mixin(config[prop], value, true);
+ }
+ } else {
+ config[prop] = value;
+ }
+ });
//Merge shim
if (cfg.shim) {
@@ -1325,8 +1284,8 @@
deps: value
};
}
- if (value.exports && !value.exports.__buildReady) {
- value.exports = context.makeShimExports(value.exports);
+ if ((value.exports || value.init) && !value.exportsFn) {
+ value.exportsFn = context.makeShimExports(value);
}
shim[id] = value;
});
@@ -1381,134 +1340,158 @@
}
},
- makeShimExports: function (exports) {
- var func;
- if (typeof exports === 'string') {
- func = function () {
- return getGlobal(exports);
- };
- //Save the exports for use in nodefine checking.
- func.exports = exports;
- return func;
- } else {
- return function () {
- return exports.apply(global, arguments);
+ makeShimExports: function (value) {
+ function fn() {
+ var ret;
+ if (value.init) {
+ ret = value.init.apply(global, arguments);
+ }
+ return ret || (value.exports && getGlobal(value.exports));
+ }
+ return fn;
+ },
+
+ makeRequire: function (relMap, options) {
+ options = options || {};
+
+ function localRequire(deps, callback, errback) {
+ var id, map, requireMod;
+
+ if (options.enableBuildCallback && callback && isFunction(callback)) {
+ callback.__requireJsBuild = true;
+ }
+
+ if (typeof deps === 'string') {
+ if (isFunction(callback)) {
+ //Invalid call
+ return onError(makeError('requireargs', 'Invalid require call'), errback);
+ }
+
+ //If require|exports|module are requested, get the
+ //value for them from the special handlers. Caveat:
+ //this only works while module is being defined.
+ if (relMap && hasProp(handlers, deps)) {
+ return handlers[deps](registry[relMap.id]);
+ }
+
+ //Synchronous access to one module. If require.get is
+ //available (as in the Node adapter), prefer that.
+ if (req.get) {
+ return req.get(context, deps, relMap, localRequire);
+ }
+
+ //Normalize module name, if it contains . or ..
+ map = makeModuleMap(deps, relMap, false, true);
+ id = map.id;
+
+ if (!hasProp(defined, id)) {
+ return onError(makeError('notloaded', 'Module name "' +
+ id +
+ '" has not been loaded yet for context: ' +
+ contextName +
+ (relMap ? '' : '. Use require([])')));
+ }
+ return defined[id];
+ }
+
+ //Grab defines waiting in the global queue.
+ intakeDefines();
+
+ //Mark all the dependencies as needing to be loaded.
+ context.nextTick(function () {
+ //Some defines could have been added since the
+ //require call, collect them.
+ intakeDefines();
+
+ requireMod = getModule(makeModuleMap(null, relMap));
+
+ //Store if map config should be applied to this require
+ //call for dependencies.
+ requireMod.skipMap = options.skipMap;
+
+ requireMod.init(deps, callback, errback, {
+ enabled: true
+ });
+
+ checkLoaded();
+ });
+
+ return localRequire;
+ }
+
+ mixin(localRequire, {
+ isBrowser: isBrowser,
+
+ /**
+ * Converts a module name + .extension into an URL path.
+ * *Requires* the use of a module name. It does not support using
+ * plain URLs like nameToUrl.
+ */
+ toUrl: function (moduleNamePlusExt) {
+ var ext,
+ index = moduleNamePlusExt.lastIndexOf('.'),
+ segment = moduleNamePlusExt.split('/')[0],
+ isRelative = segment === '.' || segment === '..';
+
+ //Have a file extension alias, and it is not the
+ //dots from a relative path.
+ if (index !== -1 && (!isRelative || index > 1)) {
+ ext = moduleNamePlusExt.substring(index, moduleNamePlusExt.length);
+ moduleNamePlusExt = moduleNamePlusExt.substring(0, index);
+ }
+
+ return context.nameToUrl(normalize(moduleNamePlusExt,
+ relMap && relMap.id, true), ext, true);
+ },
+
+ defined: function (id) {
+ return hasProp(defined, makeModuleMap(id, relMap, false, true).id);
+ },
+
+ specified: function (id) {
+ id = makeModuleMap(id, relMap, false, true).id;
+ return hasProp(defined, id) || hasProp(registry, id);
+ }
+ });
+
+ //Only allow undef on top level require calls
+ if (!relMap) {
+ localRequire.undef = function (id) {
+ //Bind any waiting define() calls to this context,
+ //fix for #408
+ takeGlobalQueue();
+
+ var map = makeModuleMap(id, relMap, true),
+ mod = getOwn(registry, id);
+
+ delete defined[id];
+ delete urlFetched[map.url];
+ delete undefEvents[id];
+
+ if (mod) {
+ //Hold on to listeners in case the
+ //module will be attempted to be reloaded
+ //using a different config.
+ if (mod.events.defined) {
+ undefEvents[id] = mod.events;
+ }
+
+ cleanRegistry(id);
+ }
};
}
- },
- requireDefined: function (id, relMap) {
- return hasProp(defined, makeModuleMap(id, relMap, false, true).id);
- },
-
- requireSpecified: function (id, relMap) {
- id = makeModuleMap(id, relMap, false, true).id;
- return hasProp(defined, id) || hasProp(registry, id);
- },
-
- require: function (deps, callback, errback, relMap) {
- var moduleName, id, map, requireMod, args;
- if (typeof deps === 'string') {
- if (isFunction(callback)) {
- //Invalid call
- return onError(makeError('requireargs', 'Invalid require call'), errback);
- }
-
- //Synchronous access to one module. If require.get is
- //available (as in the Node adapter), prefer that.
- //In this case deps is the moduleName and callback is
- //the relMap
- if (req.get) {
- return req.get(context, deps, callback);
- }
-
- //Just return the module wanted. In this scenario, the
- //second arg (if passed) is just the relMap.
- moduleName = deps;
- relMap = callback;
-
- //Normalize module name, if it contains . or ..
- map = makeModuleMap(moduleName, relMap, false, true);
- id = map.id;
-
- if (!hasProp(defined, id)) {
- return onError(makeError('notloaded', 'Module name "' +
- id +
- '" has not been loaded yet for context: ' +
- contextName));
- }
- return defined[id];
- }
-
- //Callback require. Normalize args. if callback or errback is
- //not a function, it means it is a relMap. Test errback first.
- if (errback && !isFunction(errback)) {
- relMap = errback;
- errback = undefined;
- }
- if (callback && !isFunction(callback)) {
- relMap = callback;
- callback = undefined;
- }
-
- //Any defined modules in the global queue, intake them now.
- takeGlobalQueue();
-
- //Make sure any remaining defQueue items get properly processed.
- while (defQueue.length) {
- args = defQueue.shift();
- if (args[0] === null) {
- return onError(makeError('mismatch', 'Mismatched anonymous define() module: ' + args[args.length - 1]));
- } else {
- //args are id, deps, factory. Should be normalized by the
- //define() function.
- callGetModule(args);
- }
- }
-
- //Mark all the dependencies as needing to be loaded.
- requireMod = getModule(makeModuleMap(null, relMap));
-
- requireMod.init(deps, callback, errback, {
- enabled: true
- });
-
- checkLoaded();
-
- return context.require;
- },
-
- undef: function (id) {
- //Bind any waiting define() calls to this context,
- //fix for #408
- takeGlobalQueue();
-
- var map = makeModuleMap(id, null, true),
- mod = registry[id];
-
- delete defined[id];
- delete urlFetched[map.url];
- delete undefEvents[id];
-
- if (mod) {
- //Hold on to listeners in case the
- //module will be attempted to be reloaded
- //using a different config.
- if (mod.events.defined) {
- undefEvents[id] = mod.events;
- }
-
- removeWaiting(id);
- }
+ return localRequire;
},
/**
* Called to enable a module if it is still in the registry
- * awaiting enablement. parent module is passed in for context,
- * used by the optimizer.
+ * awaiting enablement. A second arg, parent, the parent module,
+ * is passed in for context, when this method is overriden by
+ * the optimizer. Not shown here to keep code compact.
*/
- enable: function (depMap, parent) {
- var mod = registry[depMap.id];
+ enable: function (depMap) {
+ var mod = getOwn(registry, depMap.id);
if (mod) {
getModule(depMap).enable();
}
@@ -1522,8 +1505,8 @@
*/
completeLoad: function (moduleName) {
var found, args, mod,
- shim = config.shim[moduleName] || {},
- shExports = shim.exports && shim.exports.exports;
+ shim = getOwn(config.shim, moduleName) || {},
+ shExports = shim.exports;
takeGlobalQueue();
@@ -1548,9 +1531,9 @@
//Do this after the cycle of callGetModule in case the result
//of those calls/init calls changes the registry.
- mod = registry[moduleName];
+ mod = getOwn(registry, moduleName);
- if (!found && !defined[moduleName] && mod && !mod.inited) {
+ if (!found && !hasProp(defined, moduleName) && mod && !mod.inited) {
if (config.enforceDefine && (!shExports || !getGlobal(shExports))) {
if (hasPathFallback(moduleName)) {
return;
@@ -1563,7 +1546,7 @@
} else {
//A script that does not call define(), so just simulate
//the call for it.
- callGetModule([moduleName, (shim.deps || []), shim.exports]);
+ callGetModule([moduleName, (shim.deps || []), shim.exportsFn]);
}
}
@@ -1571,31 +1554,13 @@
},
/**
- * Converts a module name + .extension into an URL path.
- * *Requires* the use of a module name. It does not support using
- * plain URLs like nameToUrl.
- */
- toUrl: function (moduleNamePlusExt, relModuleMap) {
- var index = moduleNamePlusExt.lastIndexOf('.'),
- ext = null;
-
- if (index !== -1) {
- ext = moduleNamePlusExt.substring(index, moduleNamePlusExt.length);
- moduleNamePlusExt = moduleNamePlusExt.substring(0, index);
- }
-
- return context.nameToUrl(normalize(moduleNamePlusExt, relModuleMap && relModuleMap.id, true),
- ext);
- },
-
- /**
* Converts a module name to a file path. Supports cases where
* moduleName may actually be just an URL.
* Note that it **does not** call normalize on the moduleName,
* it is assumed to have already been normalized. This is an
* internal API, not a public one. Use toUrl for the public API.
*/
- nameToUrl: function (moduleName, ext) {
+ nameToUrl: function (moduleName, ext, skipExt) {
var paths, pkgs, pkg, pkgPath, syms, i, parentModule, url,
parentPath;
@@ -1619,8 +1584,8 @@
//and work up from it.
for (i = syms.length; i > 0; i -= 1) {
parentModule = syms.slice(0, i).join('/');
- pkg = pkgs[parentModule];
- parentPath = paths[parentModule];
+ pkg = getOwn(pkgs, parentModule);
+ parentPath = getOwn(paths, parentModule);
if (parentPath) {
//If an array, it means there are a few choices,
//Choose the one that is desired
@@ -1644,7 +1609,7 @@
//Join the path parts together, then figure out if baseUrl is needed.
url = syms.join('/');
- url += (ext || (/\?/.test(url) ? '' : '.js'));
+ url += (ext || (/\?/.test(url) || skipExt ? '' : '.js'));
url = (url.charAt(0) === '/' || url.match(/^[\w\+\.\-]+:/) ? '' : config.baseUrl) + url;
}
@@ -1660,7 +1625,7 @@
},
/**
- * Executes a module callack function. Broken out as a separate function
+ * Executes a module callback function. Broken out as a separate function
* solely to allow the build system to sequence the files in the built
* layer in the right sequence.
*
@@ -1698,10 +1663,13 @@
onScriptError: function (evt) {
var data = getScriptData(evt);
if (!hasPathFallback(data.id)) {
- return onError(makeError('scripterror', 'Script error', evt, [data.id]));
+ return onError(makeError('scripterror', 'Script error for: ' + data.id, evt, [data.id]));
}
}
- });
+ };
+
+ context.require = context.makeRequire();
+ return context;
}
/**
@@ -1742,7 +1710,7 @@
contextName = config.context;
}
- context = contexts[contextName];
+ context = getOwn(contexts, contextName);
if (!context) {
context = contexts[contextName] = req.s.newContext(contextName);
}
@@ -1763,6 +1731,16 @@
};
/**
+ * Execute something after the current tick
+ * of the event loop. Override for other envs
+ * that have a better solution than setTimeout.
+ * @param {Function} fn function to execute later.
+ */
+ req.nextTick = typeof setTimeout !== 'undefined' ? function (fn) {
+ setTimeout(fn, 4);
+ } : function (fn) { fn(); };
+
+ /**
* Export require as a global, but only if it does not already exist.
*/
if (!require) {
@@ -1782,9 +1760,21 @@
//Create default context.
req({});
- //Exports some context-sensitive methods on global require, using
- //default context if no context specified.
- addRequireMethods(req);
+ //Exports some context-sensitive methods on global require.
+ each([
+ 'toUrl',
+ 'undef',
+ 'defined',
+ 'specified'
+ ], function (prop) {
+ //Reference from contexts instead of early binding to default context,
+ //so that during builds, the latest instance of the default context
+ //with its config gets used.
+ req[prop] = function () {
+ var ctx = contexts[defContextName];
+ return ctx.require[prop].apply(ctx, arguments);
+ };
+ });
if (isBrowser) {
head = s.head = document.getElementsByTagName('head')[0];
@@ -1802,8 +1792,19 @@
* function. Intercept/override it if you want custom error handling.
* @param {Error} err the error object.
*/
- req.onError = function (err) {
- throw err;
+ req.onError = defaultOnError;
+
+ /**
+ * Creates the node for the load command. Only used in browser envs.
+ */
+ req.createNode = function (config, moduleName, url) {
+ var node = config.xhtml ?
+ document.createElementNS('http://www.w3.org/1999/xhtml', 'html:script') :
+ document.createElement('script');
+ node.type = config.scriptType || 'text/javascript';
+ node.charset = 'utf-8';
+ node.async = true;
+ return node;
};
/**
@@ -1820,12 +1821,7 @@
node;
if (isBrowser) {
//In the browser so use a script tag
- node = config.xhtml ?
- document.createElementNS('http://www.w3.org/1999/xhtml', 'html:script') :
- document.createElement('script');
- node.type = config.scriptType || 'text/javascript';
- node.charset = 'utf-8';
- node.async = true;
+ node = req.createNode(config, moduleName, url);
node.setAttribute('data-requirecontext', context.contextName);
node.setAttribute('data-requiremodule', moduleName);
@@ -1858,7 +1854,7 @@
node.attachEvent('onreadystatechange', context.onScriptLoad);
//It would be great to add an error handler here to catch
//404s in IE9+. However, onreadystatechange will fire before
- //the error handler, so that does not help. If addEvenListener
+ //the error handler, so that does not help. If addEventListener
//is used, then IE will fire error before load, but we cannot
//use that pathway given the connect.microsoft.com issue
//mentioned above about not doing the 'script execute,
@@ -1887,16 +1883,24 @@
return node;
} else if (isWebWorker) {
- //In a web worker, use importScripts. This is not a very
- //efficient use of importScripts, importScripts will block until
- //its script is downloaded and evaluated. However, if web workers
- //are in play, the expectation that a build has been done so that
- //only one script needs to be loaded anyway. This may need to be
- //reevaluated if other use cases become common.
- importScripts(url);
+ try {
+ //In a web worker, use importScripts. This is not a very
+ //efficient use of importScripts, importScripts will block until
+ //its script is downloaded and evaluated. However, if web workers
+ //are in play, the expectation that a build has been done so that
+ //only one script needs to be loaded anyway. This may need to be
+ //reevaluated if other use cases become common.
+ importScripts(url);
- //Account for anonymous modules
- context.completeLoad(moduleName);
+ //Account for anonymous modules
+ context.completeLoad(moduleName);
+ } catch (e) {
+ context.onError(makeError('importscripts',
+ 'importScripts failed for ' +
+ moduleName + ' at ' + url,
+ e,
+ [moduleName]));
+ }
}
};
@@ -1928,24 +1932,31 @@
//baseUrl, if it is not already set.
dataMain = script.getAttribute('data-main');
if (dataMain) {
+ //Preserve dataMain in case it is a path (i.e. contains '?')
+ mainScript = dataMain;
+
//Set final baseUrl if there is not already an explicit one.
if (!cfg.baseUrl) {
//Pull off the directory of data-main for use as the
//baseUrl.
- src = dataMain.split('/');
+ src = mainScript.split('/');
mainScript = src.pop();
subPath = src.length ? src.join('/') + '/' : './';
cfg.baseUrl = subPath;
- dataMain = mainScript;
}
- //Strip off any trailing .js since dataMain is now
+ //Strip off any trailing .js since mainScript is now
//like a module name.
- dataMain = dataMain.replace(jsSuffixRegExp, '');
+ mainScript = mainScript.replace(jsSuffixRegExp, '');
+
+ //If mainScript is still a path, fall back to dataMain
+ if (req.jsExtRegExp.test(mainScript)) {
+ mainScript = dataMain;
+ }
//Put the data-main script in the files to load.
- cfg.deps = cfg.deps ? cfg.deps.concat(dataMain) : [dataMain];
+ cfg.deps = cfg.deps ? cfg.deps.concat(mainScript) : [mainScript];
return true;
}
@@ -1962,7 +1973,7 @@
define = function (name, deps, callback) {
var node, context;
- //Allow for anonymous functions
+ //Allow for anonymous modules
if (typeof name !== 'string') {
//Adjust args appropriately
callback = deps;
@@ -1973,12 +1984,13 @@
//This module may not have dependencies
if (!isArray(deps)) {
callback = deps;
- deps = [];
+ deps = null;
}
//If no name, and callback is a function, then figure out if it a
//CommonJS thing with dependencies.
- if (!deps.length && isFunction(callback)) {
+ if (!deps && isFunction(callback)) {
+ deps = [];
//Remove comments from the callback string,
//look for require calls, and pull them into the dependencies,
//but only if there are function args.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: JS libraries: update jStorage to 4.4
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8ab88925e5ef/
Changeset: 8ab88925e5ef
User: carlfeberhard
Date: 2013-08-21 17:47:11
Summary: JS libraries: update jStorage to 4.4
Affected #: 3 files
diff -r c528daf3e3b3936dc399d6da4cfe4e636f4a556c -r 8ab88925e5eff54a056722bdf0fb3622d0a0455c static/scripts/libs/jquery/jstorage.js
--- a/static/scripts/libs/jquery/jstorage.js
+++ b/static/scripts/libs/jquery/jstorage.js
@@ -3,7 +3,7 @@
* Simple local storage wrapper to save data on the browser side, supporting
* all major browsers - IE6+, Firefox2+, Safari4+, Chrome4+ and Opera 10.5+
*
- * Copyright (c) 2010 Andris Reinman, andris.reinman(a)gmail.com
+ * Copyright (c) 2010 - 2012 Andris Reinman, andris.reinman(a)gmail.com
* Project homepage: www.jstorage.info
*
* Licensed under MIT-style license:
@@ -24,78 +24,66 @@
* SOFTWARE.
*/
-/**
- * $.jStorage
- *
- * USAGE:
- *
- * jStorage requires Prototype, MooTools or jQuery! If jQuery is used, then
- * jQuery-JSON (http://code.google.com/p/jquery-json/) is also needed.
- * (jQuery-JSON needs to be loaded BEFORE jStorage!)
- *
- * Methods:
- *
- * -set(key, value)
- * $.jStorage.set(key, value) -> saves a value
- *
- * -get(key[, default])
- * value = $.jStorage.get(key [, default]) ->
- * retrieves value if key exists, or default if it doesn't
- *
- * -deleteKey(key)
- * $.jStorage.deleteKey(key) -> removes a key from the storage
- *
- * -flush()
- * $.jStorage.flush() -> clears the cache
- *
- * -storageObj()
- * $.jStorage.storageObj() -> returns a read-ony copy of the actual storage
- *
- * -storageSize()
- * $.jStorage.storageSize() -> returns the size of the storage in bytes
- *
- * -index()
- * $.jStorage.index() -> returns the used keys as an array
- *
- * -storageAvailable()
- * $.jStorage.storageAvailable() -> returns true if storage is available
- *
- * -reInit()
- * $.jStorage.reInit() -> reloads the data from browser storage
- *
- * <value> can be any JSON-able value, including objects and arrays.
- *
- **/
+ (function(){
+ var
+ /* jStorage version */
+ JSTORAGE_VERSION = "0.4.4",
-(function($){
- if(!$ || !($.toJSON || Object.toJSON || window.JSON)){
- throw new Error("jQuery, MooTools or Prototype needs to be loaded before jStorage!");
+ /* detect a dollar object or create one if not found */
+ $ = window.jQuery || window.$ || (window.$ = {}),
+
+ /* check for a JSON handling support */
+ JSON = {
+ parse:
+ window.JSON && (window.JSON.parse || window.JSON.decode) ||
+ String.prototype.evalJSON && function(str){return String(str).evalJSON();} ||
+ $.parseJSON ||
+ $.evalJSON,
+ stringify:
+ Object.toJSON ||
+ window.JSON && (window.JSON.stringify || window.JSON.encode) ||
+ $.toJSON
+ };
+
+ // Break if no JSON support was found
+ if(!('parse' in JSON) || !('stringify' in JSON)){
+ throw new Error("No JSON support found, include //cdnjs.cloudflare.com/ajax/libs/json2/20110223/json2.js to page");
}
-
+
var
- /* This is the object, that holds the cached values */
- _storage = {},
+ /* This is the object, that holds the cached values */
+ _storage = {__jstorage_meta:{CRC32:{}}},
/* Actual browser storage (localStorage or globalStorage['domain']) */
_storage_service = {jStorage:"{}"},
/* DOM element for older IE versions, holds userData behavior */
_storage_elm = null,
-
+
/* How much space does the storage take */
_storage_size = 0,
- /* function to encode objects to JSON strings */
- json_encode = $.toJSON || Object.toJSON || (window.JSON && (JSON.encode || JSON.stringify)),
+ /* which backend is currently used */
+ _backend = false,
- /* function to decode objects from JSON strings */
- json_decode = $.evalJSON || (window.JSON && (JSON.decode || JSON.parse)) || function(str){
- return String(str).evalJSON();
- },
-
- /* which backend is currently used */
- _backend = false;
-
+ /* onchange observers */
+ _observers = {},
+
+ /* timeout to wait after onchange event */
+ _observer_timeout = false,
+
+ /* last update time */
+ _observer_update = 0,
+
+ /* pubsub observers */
+ _pubsub_observers = {},
+
+ /* skip published items older than current timestamp */
+ _pubsub_last = +new Date(),
+
+ /* Next check for TTL */
+ _ttl_timeout,
+
/**
* XML encoding and decoding as XML nodes can't be JSON'ized
* XML nodes are encoded and decoded if the node is the value to be saved
@@ -105,7 +93,7 @@
* $.jStorage.set("key", {xml: xmlNode}); // NOT OK
*/
_XMLService = {
-
+
/**
* Validates a XML node to be XML
* based on jQuery.isXML function
@@ -114,7 +102,7 @@
var documentElement = (elm ? elm.ownerDocument || elm : 0).documentElement;
return documentElement ? documentElement.nodeName !== "HTML" : false;
},
-
+
/**
* Encodes a XML node to string
* based on http://www.mercurytide.co.uk/news/article/issues-when-working-ajax/
@@ -132,7 +120,7 @@
}
return false;
},
-
+
/**
* Decodes a XML node from string
* loosely based on http://outwestmedia.com/jquery-plugins/xmldom/
@@ -154,20 +142,33 @@
}
};
+
////////////////////////// PRIVATE METHODS ////////////////////////
/**
* Initialization function. Detects if the browser supports DOM Storage
* or userData behavior and behaves accordingly.
- * @returns undefined
*/
function _init(){
/* Check if browser supports localStorage */
+ var localStorageReallyWorks = false;
if("localStorage" in window){
try {
+ window.localStorage.setItem('_tmptest', 'tmpval');
+ localStorageReallyWorks = true;
+ window.localStorage.removeItem('_tmptest');
+ } catch(BogusQuotaExceededErrorOnIos5) {
+ // Thanks be to iOS5 Private Browsing mode which throws
+ // QUOTA_EXCEEDED_ERRROR DOM Exception 22.
+ }
+ }
+
+ if(localStorageReallyWorks){
+ try {
if(window.localStorage) {
_storage_service = window.localStorage;
_backend = "localStorage";
+ _observer_update = _storage_service.jStorage_update;
}
} catch(E3) {/* Firefox fails when touching localStorage and cookies are disabled */}
}
@@ -175,8 +176,14 @@
else if("globalStorage" in window){
try {
if(window.globalStorage) {
- _storage_service = window.globalStorage[window.location.hostname];
+ if(window.location.hostname == 'localhost'){
+ _storage_service = window.globalStorage['localhost.localdomain'];
+ }
+ else{
+ _storage_service = window.globalStorage[window.location.hostname];
+ }
_backend = "globalStorage";
+ _observer_update = _storage_service.jStorage_update;
}
} catch(E4) {/* Firefox fails when touching localStorage and cookies are disabled */}
}
@@ -191,11 +198,24 @@
/* userData element needs to be inserted into the DOM! */
document.getElementsByTagName('head')[0].appendChild(_storage_elm);
- _storage_elm.load("jStorage");
+ try{
+ _storage_elm.load("jStorage");
+ }catch(E){
+ // try to reset cache
+ _storage_elm.setAttribute("jStorage", "{}");
+ _storage_elm.save("jStorage");
+ _storage_elm.load("jStorage");
+ }
+
var data = "{}";
try{
data = _storage_elm.getAttribute("jStorage");
}catch(E5){}
+
+ try{
+ _observer_update = _storage_elm.getAttribute("jStorage_update");
+ }catch(E6){}
+
_storage_service.jStorage = data;
_backend = "userDataBehavior";
}else{
@@ -204,32 +224,217 @@
}
}
+ // Load data from storage
_load_storage();
+
+ // remove dead keys
+ _handleTTL();
+
+ // start listening for changes
+ _setupObserver();
+
+ // initialize publish-subscribe service
+ _handlePubSub();
+
+ // handle cached navigation
+ if("addEventListener" in window){
+ window.addEventListener("pageshow", function(event){
+ if(event.persisted){
+ _storageObserver();
+ }
+ }, false);
+ }
}
-
+
+ /**
+ * Reload data from storage when needed
+ */
+ function _reloadData(){
+ var data = "{}";
+
+ if(_backend == "userDataBehavior"){
+ _storage_elm.load("jStorage");
+
+ try{
+ data = _storage_elm.getAttribute("jStorage");
+ }catch(E5){}
+
+ try{
+ _observer_update = _storage_elm.getAttribute("jStorage_update");
+ }catch(E6){}
+
+ _storage_service.jStorage = data;
+ }
+
+ _load_storage();
+
+ // remove dead keys
+ _handleTTL();
+
+ _handlePubSub();
+ }
+
+ /**
+ * Sets up a storage change observer
+ */
+ function _setupObserver(){
+ if(_backend == "localStorage" || _backend == "globalStorage"){
+ if("addEventListener" in window){
+ window.addEventListener("storage", _storageObserver, false);
+ }else{
+ document.attachEvent("onstorage", _storageObserver);
+ }
+ }else if(_backend == "userDataBehavior"){
+ setInterval(_storageObserver, 1000);
+ }
+ }
+
+ /**
+ * Fired on any kind of data change, needs to check if anything has
+ * really been changed
+ */
+ function _storageObserver(){
+ var updateTime;
+ // cumulate change notifications with timeout
+ clearTimeout(_observer_timeout);
+ _observer_timeout = setTimeout(function(){
+
+ if(_backend == "localStorage" || _backend == "globalStorage"){
+ updateTime = _storage_service.jStorage_update;
+ }else if(_backend == "userDataBehavior"){
+ _storage_elm.load("jStorage");
+ try{
+ updateTime = _storage_elm.getAttribute("jStorage_update");
+ }catch(E5){}
+ }
+
+ if(updateTime && updateTime != _observer_update){
+ _observer_update = updateTime;
+ _checkUpdatedKeys();
+ }
+
+ }, 25);
+ }
+
+ /**
+ * Reloads the data and checks if any keys are changed
+ */
+ function _checkUpdatedKeys(){
+ var oldCrc32List = JSON.parse(JSON.stringify(_storage.__jstorage_meta.CRC32)),
+ newCrc32List;
+
+ _reloadData();
+ newCrc32List = JSON.parse(JSON.stringify(_storage.__jstorage_meta.CRC32));
+
+ var key,
+ updated = [],
+ removed = [];
+
+ for(key in oldCrc32List){
+ if(oldCrc32List.hasOwnProperty(key)){
+ if(!newCrc32List[key]){
+ removed.push(key);
+ continue;
+ }
+ if(oldCrc32List[key] != newCrc32List[key] && String(oldCrc32List[key]).substr(0,2) == "2."){
+ updated.push(key);
+ }
+ }
+ }
+
+ for(key in newCrc32List){
+ if(newCrc32List.hasOwnProperty(key)){
+ if(!oldCrc32List[key]){
+ updated.push(key);
+ }
+ }
+ }
+
+ _fireObservers(updated, "updated");
+ _fireObservers(removed, "deleted");
+ }
+
+ /**
+ * Fires observers for updated keys
+ *
+ * @param {Array|String} keys Array of key names or a key
+ * @param {String} action What happened with the value (updated, deleted, flushed)
+ */
+ function _fireObservers(keys, action){
+ keys = [].concat(keys || []);
+ if(action == "flushed"){
+ keys = [];
+ for(var key in _observers){
+ if(_observers.hasOwnProperty(key)){
+ keys.push(key);
+ }
+ }
+ action = "deleted";
+ }
+ for(var i=0, len = keys.length; i<len; i++){
+ if(_observers[keys[i]]){
+ for(var j=0, jlen = _observers[keys[i]].length; j<jlen; j++){
+ _observers[keys[i]][j](keys[i], action);
+ }
+ }
+ if(_observers["*"]){
+ for(var j=0, jlen = _observers["*"].length; j<jlen; j++){
+ _observers["*"][j](keys[i], action);
+ }
+ }
+ }
+ }
+
+ /**
+ * Publishes key change to listeners
+ */
+ function _publishChange(){
+ var updateTime = (+new Date()).toString();
+
+ if(_backend == "localStorage" || _backend == "globalStorage"){
+ try {
+ _storage_service.jStorage_update = updateTime;
+ } catch (E8) {
+ // safari private mode has been enabled after the jStorage initialization
+ _backend = false;
+ }
+ }else if(_backend == "userDataBehavior"){
+ _storage_elm.setAttribute("jStorage_update", updateTime);
+ _storage_elm.save("jStorage");
+ }
+
+ _storageObserver();
+ }
+
/**
* Loads the data from the storage based on the supported mechanism
- * @returns undefined
*/
function _load_storage(){
/* if jStorage string is retrieved, then decode it */
if(_storage_service.jStorage){
try{
- _storage = json_decode(String(_storage_service.jStorage));
+ _storage = JSON.parse(String(_storage_service.jStorage));
}catch(E6){_storage_service.jStorage = "{}";}
}else{
_storage_service.jStorage = "{}";
}
- _storage_size = _storage_service.jStorage?String(_storage_service.jStorage).length:0;
+ _storage_size = _storage_service.jStorage?String(_storage_service.jStorage).length:0;
+
+ if(!_storage.__jstorage_meta){
+ _storage.__jstorage_meta = {};
+ }
+ if(!_storage.__jstorage_meta.CRC32){
+ _storage.__jstorage_meta.CRC32 = {};
+ }
}
/**
* This functions provides the "save" mechanism to store the jStorage object
- * @returns undefined
*/
function _save(){
+ _dropOldEvents(); // remove expired events
try{
- _storage_service.jStorage = json_encode(_storage);
+ _storage_service.jStorage = JSON.stringify(_storage);
// If userData is used as the storage engine, additional
if(_storage_elm) {
_storage_elm.setAttribute("jStorage",_storage_service.jStorage);
@@ -241,52 +446,256 @@
/**
* Function checks if a key is set and is string or numberic
+ *
+ * @param {String} key Key name
*/
function _checkKey(key){
if(!key || (typeof key != "string" && typeof key != "number")){
throw new TypeError('Key name must be string or numeric');
}
+ if(key == "__jstorage_meta"){
+ throw new TypeError('Reserved key name');
+ }
return true;
}
+ /**
+ * Removes expired keys
+ */
+ function _handleTTL(){
+ var curtime, i, TTL, CRC32, nextExpire = Infinity, changed = false, deleted = [];
+
+ clearTimeout(_ttl_timeout);
+
+ if(!_storage.__jstorage_meta || typeof _storage.__jstorage_meta.TTL != "object"){
+ // nothing to do here
+ return;
+ }
+
+ curtime = +new Date();
+ TTL = _storage.__jstorage_meta.TTL;
+
+ CRC32 = _storage.__jstorage_meta.CRC32;
+ for(i in TTL){
+ if(TTL.hasOwnProperty(i)){
+ if(TTL[i] <= curtime){
+ delete TTL[i];
+ delete CRC32[i];
+ delete _storage[i];
+ changed = true;
+ deleted.push(i);
+ }else if(TTL[i] < nextExpire){
+ nextExpire = TTL[i];
+ }
+ }
+ }
+
+ // set next check
+ if(nextExpire != Infinity){
+ _ttl_timeout = setTimeout(_handleTTL, nextExpire - curtime);
+ }
+
+ // save changes
+ if(changed){
+ _save();
+ _publishChange();
+ _fireObservers(deleted, "deleted");
+ }
+ }
+
+ /**
+ * Checks if there's any events on hold to be fired to listeners
+ */
+ function _handlePubSub(){
+ var i, len;
+ if(!_storage.__jstorage_meta.PubSub){
+ return;
+ }
+ var pubelm,
+ _pubsubCurrent = _pubsub_last;
+
+ for(i=len=_storage.__jstorage_meta.PubSub.length-1; i>=0; i--){
+ pubelm = _storage.__jstorage_meta.PubSub[i];
+ if(pubelm[0] > _pubsub_last){
+ _pubsubCurrent = pubelm[0];
+ _fireSubscribers(pubelm[1], pubelm[2]);
+ }
+ }
+
+ _pubsub_last = _pubsubCurrent;
+ }
+
+ /**
+ * Fires all subscriber listeners for a pubsub channel
+ *
+ * @param {String} channel Channel name
+ * @param {Mixed} payload Payload data to deliver
+ */
+ function _fireSubscribers(channel, payload){
+ if(_pubsub_observers[channel]){
+ for(var i=0, len = _pubsub_observers[channel].length; i<len; i++){
+ // send immutable data that can't be modified by listeners
+ _pubsub_observers[channel][i](channel, JSON.parse(JSON.stringify(payload)));
+ }
+ }
+ }
+
+ /**
+ * Remove old events from the publish stream (at least 2sec old)
+ */
+ function _dropOldEvents(){
+ if(!_storage.__jstorage_meta.PubSub){
+ return;
+ }
+
+ var retire = +new Date() - 2000;
+
+ for(var i=0, len = _storage.__jstorage_meta.PubSub.length; i<len; i++){
+ if(_storage.__jstorage_meta.PubSub[i][0] <= retire){
+ // deleteCount is needed for IE6
+ _storage.__jstorage_meta.PubSub.splice(i, _storage.__jstorage_meta.PubSub.length - i);
+ break;
+ }
+ }
+
+ if(!_storage.__jstorage_meta.PubSub.length){
+ delete _storage.__jstorage_meta.PubSub;
+ }
+
+ }
+
+ /**
+ * Publish payload to a channel
+ *
+ * @param {String} channel Channel name
+ * @param {Mixed} payload Payload to send to the subscribers
+ */
+ function _publish(channel, payload){
+ if(!_storage.__jstorage_meta){
+ _storage.__jstorage_meta = {};
+ }
+ if(!_storage.__jstorage_meta.PubSub){
+ _storage.__jstorage_meta.PubSub = [];
+ }
+
+ _storage.__jstorage_meta.PubSub.unshift([+new Date, channel, payload]);
+
+ _save();
+ _publishChange();
+ }
+
+
+ /**
+ * JS Implementation of MurmurHash2
+ *
+ * SOURCE: https://github.com/garycourt/murmurhash-js (MIT licensed)
+ *
+ * @author <a href="mailto:gary.court@gmail.com">Gary Court</a>
+ * @see http://github.com/garycourt/murmurhash-js
+ * @author <a href="mailto:aappleby@gmail.com">Austin Appleby</a>
+ * @see http://sites.google.com/site/murmurhash/
+ *
+ * @param {string} str ASCII only
+ * @param {number} seed Positive integer only
+ * @return {number} 32-bit positive integer hash
+ */
+
+ function murmurhash2_32_gc(str, seed) {
+ var
+ l = str.length,
+ h = seed ^ l,
+ i = 0,
+ k;
+
+ while (l >= 4) {
+ k =
+ ((str.charCodeAt(i) & 0xff)) |
+ ((str.charCodeAt(++i) & 0xff) << 8) |
+ ((str.charCodeAt(++i) & 0xff) << 16) |
+ ((str.charCodeAt(++i) & 0xff) << 24);
+
+ k = (((k & 0xffff) * 0x5bd1e995) + ((((k >>> 16) * 0x5bd1e995) & 0xffff) << 16));
+ k ^= k >>> 24;
+ k = (((k & 0xffff) * 0x5bd1e995) + ((((k >>> 16) * 0x5bd1e995) & 0xffff) << 16));
+
+ h = (((h & 0xffff) * 0x5bd1e995) + ((((h >>> 16) * 0x5bd1e995) & 0xffff) << 16)) ^ k;
+
+ l -= 4;
+ ++i;
+ }
+
+ switch (l) {
+ case 3: h ^= (str.charCodeAt(i + 2) & 0xff) << 16;
+ case 2: h ^= (str.charCodeAt(i + 1) & 0xff) << 8;
+ case 1: h ^= (str.charCodeAt(i) & 0xff);
+ h = (((h & 0xffff) * 0x5bd1e995) + ((((h >>> 16) * 0x5bd1e995) & 0xffff) << 16));
+ }
+
+ h ^= h >>> 13;
+ h = (((h & 0xffff) * 0x5bd1e995) + ((((h >>> 16) * 0x5bd1e995) & 0xffff) << 16));
+ h ^= h >>> 15;
+
+ return h >>> 0;
+ }
+
////////////////////////// PUBLIC INTERFACE /////////////////////////
$.jStorage = {
/* Version number */
- version: "0.1.5.0",
+ version: JSTORAGE_VERSION,
/**
* Sets a key's value.
- *
- * @param {String} key - Key to set. If this value is not set or not
+ *
+ * @param {String} key Key to set. If this value is not set or not
* a string an exception is raised.
- * @param value - Value to set. This can be any value that is JSON
+ * @param {Mixed} value Value to set. This can be any value that is JSON
* compatible (Numbers, Strings, Objects etc.).
- * @returns the used value
+ * @param {Object} [options] - possible options to use
+ * @param {Number} [options.TTL] - optional TTL value
+ * @return {Mixed} the used value
*/
- set: function(key, value){
+ set: function(key, value, options){
_checkKey(key);
+
+ options = options || {};
+
+ // undefined values are deleted automatically
+ if(typeof value == "undefined"){
+ this.deleteKey(key);
+ return value;
+ }
+
if(_XMLService.isXML(value)){
value = {_is_xml:true,xml:_XMLService.encode(value)};
+ }else if(typeof value == "function"){
+ return undefined; // functions can't be saved!
+ }else if(value && typeof value == "object"){
+ // clone the object before saving to _storage tree
+ value = JSON.parse(JSON.stringify(value));
}
+
_storage[key] = value;
- _save();
+
+ _storage.__jstorage_meta.CRC32[key] = "2." + murmurhash2_32_gc(JSON.stringify(value), 0x9747b28c);
+
+ this.setTTL(key, options.TTL || 0); // also handles saving and _publishChange
+
+ _fireObservers(key, "updated");
return value;
},
-
+
/**
* Looks up a key in cache
- *
+ *
* @param {String} key - Key to look up.
* @param {mixed} def - Default value to return, if key didn't exist.
- * @returns the key value, default value or <null>
+ * @return {Mixed} the key value, default value or null
*/
get: function(key, def){
_checkKey(key);
if(key in _storage){
- if(typeof _storage[key] == "object" &&
- _storage[key]._is_xml &&
- _storage[key]._is_xml){
+ if(_storage[key] && typeof _storage[key] == "object" && _storage[key]._is_xml) {
return _XMLService.decode(_storage[key].xml);
}else{
return _storage[key];
@@ -294,127 +703,231 @@
}
return typeof(def) == 'undefined' ? null : def;
},
-
+
/**
* Deletes a key from cache.
- *
+ *
* @param {String} key - Key to delete.
- * @returns true if key existed or false if it didn't
+ * @return {Boolean} true if key existed or false if it didn't
*/
deleteKey: function(key){
_checkKey(key);
if(key in _storage){
delete _storage[key];
+ // remove from TTL list
+ if(typeof _storage.__jstorage_meta.TTL == "object" &&
+ key in _storage.__jstorage_meta.TTL){
+ delete _storage.__jstorage_meta.TTL[key];
+ }
+
+ delete _storage.__jstorage_meta.CRC32[key];
+
_save();
+ _publishChange();
+ _fireObservers(key, "deleted");
return true;
}
return false;
},
/**
+ * Sets a TTL for a key, or remove it if ttl value is 0 or below
+ *
+ * @param {String} key - key to set the TTL for
+ * @param {Number} ttl - TTL timeout in milliseconds
+ * @return {Boolean} true if key existed or false if it didn't
+ */
+ setTTL: function(key, ttl){
+ var curtime = +new Date();
+ _checkKey(key);
+ ttl = Number(ttl) || 0;
+ if(key in _storage){
+
+ if(!_storage.__jstorage_meta.TTL){
+ _storage.__jstorage_meta.TTL = {};
+ }
+
+ // Set TTL value for the key
+ if(ttl>0){
+ _storage.__jstorage_meta.TTL[key] = curtime + ttl;
+ }else{
+ delete _storage.__jstorage_meta.TTL[key];
+ }
+
+ _save();
+
+ _handleTTL();
+
+ _publishChange();
+ return true;
+ }
+ return false;
+ },
+
+ /**
+ * Gets remaining TTL (in milliseconds) for a key or 0 when no TTL has been set
+ *
+ * @param {String} key Key to check
+ * @return {Number} Remaining TTL in milliseconds
+ */
+ getTTL: function(key){
+ var curtime = +new Date(), ttl;
+ _checkKey(key);
+ if(key in _storage && _storage.__jstorage_meta.TTL && _storage.__jstorage_meta.TTL[key]){
+ ttl = _storage.__jstorage_meta.TTL[key] - curtime;
+ return ttl || 0;
+ }
+ return 0;
+ },
+
+ /**
* Deletes everything in cache.
- *
- * @returns true
+ *
+ * @return {Boolean} Always true
*/
flush: function(){
- _storage = {};
+ _storage = {__jstorage_meta:{CRC32:{}}};
_save();
- /*
- * Just to be sure - andris9/jStorage#3
- */
- try{
- window.localStorage.clear();
- }catch(E8){}
+ _publishChange();
+ _fireObservers(null, "flushed");
return true;
},
-
+
/**
* Returns a read-only copy of _storage
- *
- * @returns Object
+ *
+ * @return {Object} Read-only copy of _storage
*/
storageObj: function(){
function F() {}
F.prototype = _storage;
return new F();
},
-
+
/**
* Returns an index of all used keys as an array
* ['key1', 'key2',..'keyN']
- *
- * @returns Array
+ *
+ * @return {Array} Used keys
*/
index: function(){
var index = [], i;
for(i in _storage){
- if(_storage.hasOwnProperty(i)){
+ if(_storage.hasOwnProperty(i) && i != "__jstorage_meta"){
index.push(i);
}
}
return index;
},
-
+
/**
* How much space in bytes does the storage take?
- *
- * @returns Number
+ *
+ * @return {Number} Storage size in chars (not the same as in bytes,
+ * since some chars may take several bytes)
*/
storageSize: function(){
return _storage_size;
},
-
+
/**
* Which backend is currently in use?
- *
- * @returns String
+ *
+ * @return {String} Backend name
*/
currentBackend: function(){
return _backend;
},
-
+
/**
* Test if storage is available
- *
- * @returns Boolean
+ *
+ * @return {Boolean} True if storage can be used
*/
storageAvailable: function(){
return !!_backend;
},
-
+
+ /**
+ * Register change listeners
+ *
+ * @param {String} key Key name
+ * @param {Function} callback Function to run when the key changes
+ */
+ listenKeyChange: function(key, callback){
+ _checkKey(key);
+ if(!_observers[key]){
+ _observers[key] = [];
+ }
+ _observers[key].push(callback);
+ },
+
+ /**
+ * Remove change listeners
+ *
+ * @param {String} key Key name to unregister listeners against
+ * @param {Function} [callback] If set, unregister the callback, if not - unregister all
+ */
+ stopListening: function(key, callback){
+ _checkKey(key);
+
+ if(!_observers[key]){
+ return;
+ }
+
+ if(!callback){
+ delete _observers[key];
+ return;
+ }
+
+ for(var i = _observers[key].length - 1; i>=0; i--){
+ if(_observers[key][i] == callback){
+ _observers[key].splice(i,1);
+ }
+ }
+ },
+
+ /**
+ * Subscribe to a Publish/Subscribe event stream
+ *
+ * @param {String} channel Channel name
+ * @param {Function} callback Function to run when the something is published to the channel
+ */
+ subscribe: function(channel, callback){
+ channel = (channel || "").toString();
+ if(!channel){
+ throw new TypeError('Channel not defined');
+ }
+ if(!_pubsub_observers[channel]){
+ _pubsub_observers[channel] = [];
+ }
+ _pubsub_observers[channel].push(callback);
+ },
+
+ /**
+ * Publish data to an event stream
+ *
+ * @param {String} channel Channel name
+ * @param {Mixed} payload Payload to deliver
+ */
+ publish: function(channel, payload){
+ channel = (channel || "").toString();
+ if(!channel){
+ throw new TypeError('Channel not defined');
+ }
+
+ _publish(channel, payload);
+ },
+
/**
* Reloads the data from browser storage
- *
- * @returns undefined
*/
reInit: function(){
- var new_storage_elm, data;
- if(_storage_elm && _storage_elm.addBehavior){
- new_storage_elm = document.createElement('link');
-
- _storage_elm.parentNode.replaceChild(new_storage_elm, _storage_elm);
- _storage_elm = new_storage_elm;
-
- /* Use a DOM element to act as userData storage */
- _storage_elm.style.behavior = 'url(#default#userData)';
-
- /* userData element needs to be inserted into the DOM! */
- document.getElementsByTagName('head')[0].appendChild(_storage_elm);
-
- _storage_elm.load("jStorage");
- data = "{}";
- try{
- data = _storage_elm.getAttribute("jStorage");
- }catch(E5){}
- _storage_service.jStorage = data;
- _backend = "userDataBehavior";
- }
-
- _load_storage();
+ _reloadData();
}
};
// Initialize jStorage
_init();
-})(window.jQuery || window.$);
\ No newline at end of file
+})();
diff -r c528daf3e3b3936dc399d6da4cfe4e636f4a556c -r 8ab88925e5eff54a056722bdf0fb3622d0a0455c static/scripts/mvc/base-mvc.js
--- a/static/scripts/mvc/base-mvc.js
+++ b/static/scripts/mvc/base-mvc.js
@@ -196,10 +196,14 @@
storageDefaults = storageDefaults || {};
// ~constants for the current engine
- //TODO:?? this would be greatly simplified if we're IE9+ only (setters/getters)
- var STORAGE_ENGINE_GETTER = jQuery.jStorage.get,
- STORAGE_ENGINE_SETTER = jQuery.jStorage.set,
- STORAGE_ENGINE_KEY_DELETER = jQuery.jStorage.deleteKey;
+ var STORAGE_ENGINE = sessionStorage,
+ STORAGE_ENGINE_GETTER = function sessionStorageGet( key ){
+ return JSON.parse( this.getItem( key ) );
+ },
+ STORAGE_ENGINE_SETTER = function sessionStorageSet( key, val ){
+ return this.setItem( key, JSON.stringify( val ) );
+ },
+ STORAGE_ENGINE_KEY_DELETER = function sessionStorageDel( key ){ return this.removeItem( key ); };
/** Inner, recursive, private class for method chaining access.
* @name StorageRecursionHelper
@@ -258,18 +262,16 @@
//??: more readable to make another class?
var returnedStorage = {};
// attempt to get starting data from engine...
- data = STORAGE_ENGINE_GETTER( storageKey );
+ data = STORAGE_ENGINE_GETTER.call( STORAGE_ENGINE, storageKey );
// ...if that fails, use the defaults (and store them)
- if( data === null ){
- //console.debug( 'no previous data. using defaults...' );
+ if( data === null || data === undefined ){
data = jQuery.extend( true, {}, storageDefaults );
- STORAGE_ENGINE_SETTER( storageKey, data );
+ STORAGE_ENGINE_SETTER.call( STORAGE_ENGINE, storageKey, data );
}
// the object returned by this constructor will be a modified StorageRecursionHelper
returnedStorage = new StorageRecursionHelper( data );
-
jQuery.extend( returnedStorage, /** @lends PersistantStorage.prototype */{
/** The base case for save()'s upward recursion - save everything to storage.
* @private
@@ -277,13 +279,13 @@
*/
_save : function( newData ){
//console.debug( returnedStorage, '._save:', JSON.stringify( returnedStorage.get() ) );
- return STORAGE_ENGINE_SETTER( storageKey, returnedStorage.get() );
+ return STORAGE_ENGINE_SETTER.call( STORAGE_ENGINE, storageKey, returnedStorage.get() );
},
/** Delete function to remove the entire base data object from the storageEngine.
*/
destroy : function(){
//console.debug( returnedStorage, '.destroy:' );
- return STORAGE_ENGINE_KEY_DELETER( storageKey );
+ return STORAGE_ENGINE_KEY_DELETER.call( STORAGE_ENGINE, storageKey );
},
/** String representation.
*/
diff -r c528daf3e3b3936dc399d6da4cfe4e636f4a556c -r 8ab88925e5eff54a056722bdf0fb3622d0a0455c static/scripts/packed/mvc/base-mvc.js
--- a/static/scripts/packed/mvc/base-mvc.js
+++ b/static/scripts/packed/mvc/base-mvc.js
@@ -1,1 +1,1 @@
-var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;function e(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this._save();return this},deleteKey:function(j){delete i[j];this._save();return this},_save:function(){return h._save()},toString:function(){return("StorageRecursionHelper("+i+")")}}}var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);jQuery.extend(f,{_save:function(h){return c(g,f.get())},destroy:function(){return a(g)},toString:function(){return"PersistantStorage("+g+")"}});return f};
\ No newline at end of file
+var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(j,g){if(!j){throw ("PersistantStorage needs storageKey argument")}g=g||{};var h=sessionStorage,c=function i(l){return JSON.parse(this.getItem(l))},b=function e(l,m){return this.setItem(l,JSON.stringify(m))},d=function f(l){return this.removeItem(l)};function a(m,l){m=m||{};l=l||null;return{get:function(n){if(n===undefined){return m}else{if(m.hasOwnProperty(n)){return(jQuery.type(m[n])==="object")?(new a(m[n],this)):(m[n])}}return undefined},set:function(n,o){m[n]=o;this._save();return this},deleteKey:function(n){delete m[n];this._save();return this},_save:function(){return l._save()},toString:function(){return("StorageRecursionHelper("+m+")")}}}var k={};data=c.call(h,j);if(data===null||data===undefined){data=jQuery.extend(true,{},g);b.call(h,j,data)}k=new a(data);jQuery.extend(k,{_save:function(l){return b.call(h,j,k.get())},destroy:function(){return d.call(h,j)},toString:function(){return"PersistantStorage("+j+")"}});return k};
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Fix sucessfully typo in Galaxy middleware and a couple of comments.
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c528daf3e3b3/
Changeset: c528daf3e3b3
User: greg
Date: 2013-08-21 17:24:52
Summary: Fix sucessfully typo in Galaxy middleware and a couple of comments.
Affected #: 3 files
diff -r 3c60f6a7dedcf91ded89336252fc72346b1781f6 -r c528daf3e3b3936dc399d6da4cfe4e636f4a556c lib/galaxy/web/framework/middleware/error.py
--- a/lib/galaxy/web/framework/middleware/error.py
+++ b/lib/galaxy/web/framework/middleware/error.py
@@ -464,7 +464,7 @@
<div class="content"><h1>Internal Server Error</h1>
- <h2>Galaxy was unable to sucessfully complete your request</h2>
+ <h2>Galaxy was unable to successfully complete your request</h2><p>%s</p>
diff -r 3c60f6a7dedcf91ded89336252fc72346b1781f6 -r c528daf3e3b3936dc399d6da4cfe4e636f4a556c lib/galaxy/webapps/galaxy/api/folders.py
--- a/lib/galaxy/webapps/galaxy/api/folders.py
+++ b/lib/galaxy/webapps/galaxy/api/folders.py
@@ -78,7 +78,7 @@
status, output = trans.webapp.controllers['library_common'].create_folder( trans, 'api', real_parent_folder_id, '', **payload )
rval = []
- # SM: When a folder is sucessfully created:
+ # SM: When a folder is successfully created:
# - get all of the created folders. We know that they're
# folders, so prepend an "F" to them.
if 200 == status:
diff -r 3c60f6a7dedcf91ded89336252fc72346b1781f6 -r c528daf3e3b3936dc399d6da4cfe4e636f4a556c lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1434,7 +1434,7 @@
workflow_invocation_step.workflow_invocation = workflow_invocation
workflow_invocation_step.workflow_step = step
workflow_invocation_step.job = job
- # All jobs ran sucessfully, so we can save now
+ # All jobs ran successfully, so we can save now
trans.sa_session.add( workflow_invocation )
invocations.append({'outputs': outputs,
'new_history': new_history})
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Prevent parameter mismatch from preventing display of svg and throwing exception. Still needs to be handled gracefully w/ defaults -- see comment.
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3c60f6a7dedc/
Changeset: 3c60f6a7dedc
User: dannon
Date: 2013-08-21 15:57:53
Summary: Prevent parameter mismatch from preventing display of svg and throwing exception. Still needs to be handled gracefully w/ defaults -- see comment.
Affected #: 1 file
diff -r 706834360e2ace3d41146ff60d252715c5b726f1 -r 3c60f6a7dedcf91ded89336252fc72346b1781f6 lib/tool_shed/util/workflow_util.py
--- a/lib/tool_shed/util/workflow_util.py
+++ b/lib/tool_shed/util/workflow_util.py
@@ -108,7 +108,12 @@
label=prefixed_label,
extensions=input.extensions ) )
if self.tool:
- galaxy.tools.parameters.visit_input_values( self.tool.inputs, self.state.inputs, callback )
+ try:
+ galaxy.tools.parameters.visit_input_values( self.tool.inputs, self.state.inputs, callback )
+ except:
+ # TODO have this actually use default parameters? Fix at
+ # refactor, needs to be discussed wrt: reproducibility though.
+ log.exception("Tool parse failed for %s -- this indicates incompatibility of local tool version with expected version by the workflow." % self.tool.id)
return data_inputs
def get_data_outputs( self ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Use web.url_for instead of global call in visualization controller
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/706834360e2a/
Changeset: 706834360e2a
User: guerler
Date: 2013-08-21 05:44:14
Summary: Use web.url_for instead of global call in visualization controller
Affected #: 1 file
diff -r f08aa61645ae67e8ac2c3dc94c6b79f8115b1b5a -r 706834360e2ace3d41146ff60d252715c5b726f1 lib/galaxy/webapps/galaxy/controllers/visualization.py
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -421,7 +421,7 @@
if referer is not "":
referer_message = "<a href='%s'>return to the previous page</a>" % referer
else:
- referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' )
+ referer_message = "<a href='%s'>go to Galaxy's start page</a>" % web.url_for( '/' )
# Do import.
session = trans.sa_session
@@ -512,7 +512,7 @@
self.create_item_slug( session, visualization )
session.flush()
trans.set_message( "Visualization '%s' shared with user '%s'" % ( visualization.title, other.email ) )
- return trans.response.send_redirect( url_for(controller='visualization', action='sharing', id=id ) )
+ return trans.response.send_redirect( web.url_for(controller='visualization', action='sharing', id=id ) )
return trans.fill_template( "/ind_share_base.mako",
message = msg,
messagetype = mtype,
@@ -560,7 +560,7 @@
if self.create_item_slug( trans.sa_session, visualization ):
trans.sa_session.flush()
- return_dict = { "name" : visualization.title, "link" : url_for(controller='visualization', action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) }
+ return_dict = { "name" : visualization.title, "link" : web.url_for(controller='visualization', action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) }
return return_dict
@web.expose
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Removing trackster_common.mako
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f08aa61645ae/
Changeset: f08aa61645ae
User: guerler
Date: 2013-08-21 03:23:00
Summary: Removing trackster_common.mako
Affected #: 3 files
diff -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 -r f08aa61645ae67e8ac2c3dc94c6b79f8115b1b5a templates/display_base.mako
--- a/templates/display_base.mako
+++ b/templates/display_base.mako
@@ -11,7 +11,6 @@
<%inherit file="${inherit( context )}"/><%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /><%namespace file="/display_common.mako" import="*" />
-<%namespace file="/visualization/trackster_common.mako" import="*" />
##
## Functions used by base.mako and base_panels.mako to display content.
@@ -35,7 +34,9 @@
${parent.javascripts()}
${h.js( "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating",
"galaxy.autocom_tagging" )}
- ${render_trackster_js_files()}
+
+ ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui", "libs/jquery/jquery-ui-combobox",
+ "libs/require", "libs/farbtastic" )}
<script type="text/javascript">
@@ -115,7 +116,8 @@
<%def name="stylesheets()">
${parent.stylesheets()}
${h.css( "autocomplete_tagging", "embed_item", "jquery.rating" )}
- ${render_trackster_css_files()}
+ ${h.css( "history", "autocomplete_tagging", "trackster", "library",
+ "jquery-ui/smoothness/jquery-ui" )}
<style type="text/css">
.page-body {
diff -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 -r f08aa61645ae67e8ac2c3dc94c6b79f8115b1b5a templates/webapps/galaxy/visualization/display.mako
--- a/templates/webapps/galaxy/visualization/display.mako
+++ b/templates/webapps/galaxy/visualization/display.mako
@@ -1,5 +1,4 @@
<%inherit file="/display_base.mako"/>
-<%namespace file="/visualization/trackster_common.mako" import="*" /><%def name="javascripts()"><% config = item_data %>
diff -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 -r f08aa61645ae67e8ac2c3dc94c6b79f8115b1b5a templates/webapps/galaxy/visualization/trackster_common.mako
--- a/templates/webapps/galaxy/visualization/trackster_common.mako
+++ /dev/null
@@ -1,16 +0,0 @@
-##
-## Utilities for creating Trackster visualizations.
-##
-
-## Render needed CSS files.
-<%def name="render_trackster_css_files()">
- ${h.css( "history", "autocomplete_tagging", "trackster", "library",
- "jquery-ui/smoothness/jquery-ui" )}
-</%def>
-
-
-## Render needed JavaScript files.
-<%def name="render_trackster_js_files()">
- ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui", "libs/jquery/jquery-ui-combobox",
- "libs/require", "libs/farbtastic" )}
-</%def>
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Unify parameter and url access in front end
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3a1f4df1591c/
Changeset: 3a1f4df1591c
User: guerler
Date: 2013-08-21 00:51:47
Summary: Unify parameter and url access in front end
Affected #: 32 files
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/galaxy.frame.js
--- a/static/scripts/galaxy.frame.js
+++ b/static/scripts/galaxy.frame.js
@@ -74,7 +74,7 @@
initialize : function(options)
{
// load required css files
- css.load_file(options.url.styles + "/galaxy.frame.css");
+ css.load_file(options.root + "static/style/galaxy.frame.css");
// read in defaults
if (options)
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/galaxy.panels.js
--- a/static/scripts/galaxy.panels.js
+++ b/static/scripts/galaxy.panels.js
@@ -224,7 +224,7 @@
hide_modal();
$("#overlay-background").unbind( "click.overlay" );
});
- show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + galaxy_paths.attributes.image_path + "/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) );
+ show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + galaxy_config.root + "static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) );
$("#close_button").bind( "click", function() { hide_modal(); } );
}
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/galaxy.workflow_editor.canvas.js
--- a/static/scripts/galaxy.workflow_editor.canvas.js
+++ b/static/scripts/galaxy.workflow_editor.canvas.js
@@ -200,7 +200,7 @@
.appendTo( "body" )
.append(
$("<div class='buttons'></div>").append(
- $("<img/>").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function() {
+ $("<img/>").attr("src", galaxy_config.root + 'static/images/delete_icon.png').click( function() {
$.each( terminal.connectors, function( _, x ) {
if (x) {
x.destroy();
@@ -349,13 +349,13 @@
.css( { display: 'none' } )
.append(
$("<div class='buttons'></div>").append(
- $("<img/>").attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png').click( function() {
+ $("<img/>").attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png').click( function() {
if ($.inArray(output.name, node.workflow_outputs) != -1){
node.workflow_outputs.splice($.inArray(output.name, node.workflow_outputs), 1);
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png');
}else{
node.workflow_outputs.push(output.name);
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
}
workflow.has_changes = true;
canvas_manager.draw_overview();
@@ -369,19 +369,19 @@
callout.show();
r.append(callout);
if ($.inArray(output.name, node.workflow_outputs) === -1){
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png');
}else{
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
}
r.hover(
function(){
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-yellow.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-yellow.png');
},
function(){
if ($.inArray(output.name, node.workflow_outputs) === -1){
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small-outline.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png');
}else{
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
}
});
}
@@ -657,7 +657,7 @@
if(node.post_job_actions['HideDatasetAction'+ot.name] === undefined){
node.workflow_outputs.push(ot.name);
callout = $(node.element).find('.callout.'+ot.name);
- callout.find('img').attr('src', galaxy_paths.attributes.image_path + '/fugue/asterisk-small.png');
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
workflow.has_changes = true;
}
});
@@ -852,18 +852,18 @@
f.append( title );
f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 );
var b = $("<div class='toolFormBody'></div>");
- var tmp = "<div><img height='16' align='middle' src='" +galaxy_paths.attributes.image_path+ "/loading_small_white_bg.gif'/> loading tool info...</div>";
+ var tmp = "<div><img height='16' align='middle' src='" + galaxy_config.root + "static/images/loading_small_white_bg.gif'/> loading tool info...</div>";
b.append( tmp );
node.form_html = tmp;
f.append( b );
// Fix width to computed width
// Now add floats
var buttons = $("<div class='buttons' style='float: right;'></div>");
- buttons.append( $("<img/>").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function( e ) {
+ buttons.append( $("<img/>").attr("src", galaxy_config.root + 'static/images/delete_icon.png').click( function( e ) {
node.destroy();
} ).hover(
- function() { $(this).attr( "src", galaxy_paths.attributes.image_path + "/delete_icon_dark.png" ); },
- function() { $(this).attr( "src", galaxy_paths.attributes.image_path + "/delete_icon.png" ); }
+ function() { $(this).attr( "src", galaxy_config.root + "static/images/delete_icon_dark.png" ); },
+ function() { $(this).attr( "src", galaxy_config.root + "static/images/delete_icon.png" ); }
) );
// Place inside container
f.appendTo( "#canvas-container" );
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -50,7 +50,7 @@
return this.attributes.metadata.get(attribute);
},
- urlRoot: galaxy_paths.get('datasets_url')
+ urlRoot: galaxy_config.root + "api/datasets"
});
/**
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -95,7 +95,7 @@
// set up url templates
//TODO: prob. better to put this in class scope (as the handlebars templates), but...
- // they're added to GalaxyPaths on page load (after this file is loaded)
+ // they're added to galaxy_config on page load (after this file is loaded)
if( !attributes.urlTemplates ){ throw( this + ' needs urlTemplates on initialize' ); }
if( !attributes.urlTemplates.history ){ throw( this + ' needs urlTemplates.history on initialize' ); }
if( !attributes.urlTemplates.hda ){ throw( this + ' needs urlTemplates.hda on initialize' ); }
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -138,7 +138,7 @@
}));
},
- urlRoot: galaxy_paths.get('tool_url'),
+ urlRoot: galaxy_config.root + 'api/tools',
/**
* Returns object copy, optionally including only inputs that can be sampled.
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/mvc/ui.js
--- a/static/scripts/mvc/ui.js
+++ b/static/scripts/mvc/ui.js
@@ -1,17 +1,5 @@
/**
- * necessary galaxy paths
- */
-var GalaxyPaths = Backbone.Model.extend(
-{
- defaults:
- {
- root_path: "",
- image_path: ""
- }
-});
-
-/**
- * functions for creating large ui elements
+ * functions for creating major ui elements
*/
/**
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/mvc/visualizations/scatterplotControlForm.js
--- a/static/scripts/mvc/visualizations/scatterplotControlForm.js
+++ b/static/scripts/mvc/visualizations/scatterplotControlForm.js
@@ -174,7 +174,7 @@
// render the tab controls, areas and loading indicator
this.$el.append( ScatterplotControlForm.templates.mainLayout({
- loadingIndicatorImagePath : galaxy_paths.get( 'image_path' ) + '/' + this.loadingIndicatorImage,
+ loadingIndicatorImagePath : galaxy_config.root + 'static/images/' + this.loadingIndicatorImage,
message : ''
}));
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/galaxy.frame.js
--- a/static/scripts/packed/galaxy.frame.js
+++ b/static/scripts/packed/galaxy.frame.js
@@ -1,1 +1,1 @@
-define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el:"#everything",el_header:"#masthead",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:10},cols:0,top:0,top_max:0,frame_counter:0,frame_counter_id:0,frame_list:[],galaxy_frame_shadow:null,visible:false,active:false,initialize:function(d){b.load_file(d.url.styles+"/galaxy.frame.css");if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;$(this.el).append(this.frame_template_background());$(this.el).append(this.frame_template_menu());$(this.el_header).append(this.frame_template_header());var e="#galaxy-frame-shadow";$(this.el).append(this.frame_template_shadow(e.substring(1)));this.galaxy_frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.galaxy_frame_shadow,{width:0,height:0});this.frame_list[e]=this.galaxy_frame_shadow;this.panel_refresh();this.event_initialize();$(".galaxy-frame-active").tooltip({title:"Enable/Disable Scratchbook"});$(".galaxy-frame-load").tooltip({title:"Show/Hide Scratchbook"});var c=this;$(window).resize(function(){c.panel_refresh()});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},is_mobile:function(){return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i)},event:{type:null,target:null,xy:null},event_initialize:function(){this.events={mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .galaxy-frame":"event_frame_mouse_down","mousedown .galaxy-frame-active":"event_panel_active","mousedown .galaxy-frame-load":"event_panel_load","mousedown .galaxy-frame-background":"event_panel_load","mousedown .galaxy-frame-scroll-up":"event_panel_scroll_up","mousedown .galaxy-frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"};this.delegateEvents(this.events)},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.galaxy_frame_shadow,h);this.frame_insert(this.galaxy_frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.galaxy_frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("f-toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("f-toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".galaxy-frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.galaxy_frame_shadow,c);this.frame_grid(this.galaxy_frame_shadow,d.grid_location);d.grid_location=null;$(this.galaxy_frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.galaxy_frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.galaxy_frame_shadow.grid_location,true);this.galaxy_frame_shadow.grid_location=null;$(this.galaxy_frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){$(".galaxy-frame-load .number").text(this.frame_counter);if(this.frame_counter==0){$(".galaxy-frame-load").hide()}else{$(".galaxy-frame-load").show()}if(this.top==this.options.top_min){$(".galaxy-frame-scroll-up").hide()}else{$(".galaxy-frame-scroll-up").show()}if(this.top==this.top_max){$(".galaxy-frame-scroll-down").hide()}else{$(".galaxy-frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".galaxy-frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;$(".galaxy-frame").fadeOut("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-close");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-open");$(".galaxy-frame-background").hide();$(".galaxy-frame-menu").hide()}else{this.visible=true;$(".galaxy-frame").fadeIn("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-open");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-close");$(this.galaxy_frame_shadow.id).hide();$(".galaxy-frame-background").show();this.menu_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;$(".galaxy-frame-active .icon").removeClass("f-toggle");if(this.visible){this.panel_show_hide()}}else{this.active=true;$(".galaxy-frame-active .icon").addClass("f-toggle")}},frame_new:function(d){if(!this.active){if(d.location=="center"){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}if(this.frame_counter>this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#galaxy-frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.frame_template(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=parseInt(b.get_attribute("galaxy-frame","z-index"))+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},frame_template:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="galaxy-frame f-corner"><div class="f-header f-corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content f-corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon f-corner fa-icon-resize-full"></span></div>'},frame_template_shadow:function(c){return'<div id="'+c+'" class="galaxy-frame-shadow f-corner"></div>'},frame_template_background:function(){return'<div class="galaxy-frame-background"></div>'},frame_template_header:function(){return'<div class="galaxy-frame-load f-corner"><div class="number f-corner">0</div><div class="icon fa-icon-2x"></div></div><div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;"><div class="icon fa-icon-2x fa-icon-th"></div></div>'},frame_template_menu:function(){return'<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}});
\ No newline at end of file
+define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el:"#everything",el_header:"#masthead",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:10},cols:0,top:0,top_max:0,frame_counter:0,frame_counter_id:0,frame_list:[],galaxy_frame_shadow:null,visible:false,active:false,initialize:function(d){b.load_file(d.root+"static/style/galaxy.frame.css");if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;$(this.el).append(this.frame_template_background());$(this.el).append(this.frame_template_menu());$(this.el_header).append(this.frame_template_header());var e="#galaxy-frame-shadow";$(this.el).append(this.frame_template_shadow(e.substring(1)));this.galaxy_frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.galaxy_frame_shadow,{width:0,height:0});this.frame_list[e]=this.galaxy_frame_shadow;this.panel_refresh();this.event_initialize();$(".galaxy-frame-active").tooltip({title:"Enable/Disable Scratchbook"});$(".galaxy-frame-load").tooltip({title:"Show/Hide Scratchbook"});var c=this;$(window).resize(function(){c.panel_refresh()});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},is_mobile:function(){return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i)},event:{type:null,target:null,xy:null},event_initialize:function(){this.events={mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .galaxy-frame":"event_frame_mouse_down","mousedown .galaxy-frame-active":"event_panel_active","mousedown .galaxy-frame-load":"event_panel_load","mousedown .galaxy-frame-background":"event_panel_load","mousedown .galaxy-frame-scroll-up":"event_panel_scroll_up","mousedown .galaxy-frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"};this.delegateEvents(this.events)},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.galaxy_frame_shadow,h);this.frame_insert(this.galaxy_frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.galaxy_frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("f-toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("f-toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".galaxy-frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.galaxy_frame_shadow,c);this.frame_grid(this.galaxy_frame_shadow,d.grid_location);d.grid_location=null;$(this.galaxy_frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.galaxy_frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.galaxy_frame_shadow.grid_location,true);this.galaxy_frame_shadow.grid_location=null;$(this.galaxy_frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){$(".galaxy-frame-load .number").text(this.frame_counter);if(this.frame_counter==0){$(".galaxy-frame-load").hide()}else{$(".galaxy-frame-load").show()}if(this.top==this.options.top_min){$(".galaxy-frame-scroll-up").hide()}else{$(".galaxy-frame-scroll-up").show()}if(this.top==this.top_max){$(".galaxy-frame-scroll-down").hide()}else{$(".galaxy-frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".galaxy-frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;$(".galaxy-frame").fadeOut("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-close");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-open");$(".galaxy-frame-background").hide();$(".galaxy-frame-menu").hide()}else{this.visible=true;$(".galaxy-frame").fadeIn("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-open");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-close");$(this.galaxy_frame_shadow.id).hide();$(".galaxy-frame-background").show();this.menu_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;$(".galaxy-frame-active .icon").removeClass("f-toggle");if(this.visible){this.panel_show_hide()}}else{this.active=true;$(".galaxy-frame-active .icon").addClass("f-toggle")}},frame_new:function(d){if(!this.active){if(d.location=="center"){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}if(this.frame_counter>this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#galaxy-frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.frame_template(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=parseInt(b.get_attribute("galaxy-frame","z-index"))+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},frame_template:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="galaxy-frame f-corner"><div class="f-header f-corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content f-corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon f-corner fa-icon-resize-full"></span></div>'},frame_template_shadow:function(c){return'<div id="'+c+'" class="galaxy-frame-shadow f-corner"></div>'},frame_template_background:function(){return'<div class="galaxy-frame-background"></div>'},frame_template_header:function(){return'<div class="galaxy-frame-load f-corner"><div class="number f-corner">0</div><div class="icon fa-icon-2x"></div></div><div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;"><div class="icon fa-icon-2x fa-icon-th"></div></div>'},frame_template_menu:function(){return'<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/galaxy.panels.js
--- a/static/scripts/packed/galaxy.panels.js
+++ b/static/scripts/packed/galaxy.panels.js
@@ -1,1 +1,1 @@
-!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-2*this.$dialog.offset().top-this.$footer.outerHeight()-this.$header.outerHeight())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_paths.attributes.image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery);
\ No newline at end of file
+!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-2*this.$dialog.offset().top-this.$footer.outerHeight()-this.$header.outerHeight())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_config.root+"static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery);
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/galaxy.workflow_editor.canvas.js
--- a/static/scripts/packed/galaxy.workflow_editor.canvas.js
+++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js
@@ -1,1 +1,1 @@
-function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_paths.attributes.image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
+function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/delete_icon.png").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_config.root+"static/images/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_config.root+"static/images/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_config.root+"static/images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/mvc/data.js
--- a/static/scripts/packed/mvc/data.js
+++ b/static/scripts/packed/mvc/data.js
@@ -1,1 +1,1 @@
-define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_paths.get("datasets_url")});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $("<td>").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("<td>").addClass("stringalign").text(k)}else{return $("<td>").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n<p.length;n++){if(p[n].match(o)){return n}}return -1}this.col.chrom=l("Chrom",m.column_names);this.col.start=l("Pos",m.column_names);this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.")}}if(this.col.chrom===null){console.log("TabularButtonTrackster : Chromosome column undefined.");return}if(typeof k.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=k.model.attributes.id}if(typeof k.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=k.model.attributes.url_viz}if(typeof k.model.attributes.genome_build!=="undefined"){this.genome_build=k.model.attributes.genome_build}var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(n){function m(s){return !isNaN(parseFloat(s))&&isFinite(s)}if(this.col.chrom===null){return}var r=$(n.target).parent();var o=r.children().eq(this.col.chrom).html();var i=r.children().eq(this.col.start).html();var k=this.col.end?r.children().eq(this.col.end).html():i;if(!o.match("^#")&&o!==""&&m(i)){var q={dataset_id:this.dataset_id,gene_region:o+":"+i+"-"+k};var l=r.offset();var j=l.left-10;var p=l.top-$(window).scrollTop();$("#btn_viz").css({position:"fixed",top:p+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,q,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.frame_manager.frame_new({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)});n.hide_modal()})}})},"View in new visualization":function(){var o=i+"/trackster?"+$.param(k);n.frame_manager.frame_new({title:"Trackster",type:"url",content:o});n.hide_modal()}})}});return false}}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}});
\ No newline at end of file
+define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $("<td>").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("<td>").addClass("stringalign").text(k)}else{return $("<td>").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n<p.length;n++){if(p[n].match(o)){return n}}return -1}this.col.chrom=l("Chrom",m.column_names);this.col.start=l("Pos",m.column_names);this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.")}}if(this.col.chrom===null){console.log("TabularButtonTrackster : Chromosome column undefined.");return}if(typeof k.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=k.model.attributes.id}if(typeof k.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=k.model.attributes.url_viz}if(typeof k.model.attributes.genome_build!=="undefined"){this.genome_build=k.model.attributes.genome_build}var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(n){function m(s){return !isNaN(parseFloat(s))&&isFinite(s)}if(this.col.chrom===null){return}var r=$(n.target).parent();var o=r.children().eq(this.col.chrom).html();var i=r.children().eq(this.col.start).html();var k=this.col.end?r.children().eq(this.col.end).html():i;if(!o.match("^#")&&o!==""&&m(i)){var q={dataset_id:this.dataset_id,gene_region:o+":"+i+"-"+k};var l=r.offset();var j=l.left-10;var p=l.top-$(window).scrollTop();$("#btn_viz").css({position:"fixed",top:p+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,q,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.frame_manager.frame_new({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)});n.hide_modal()})}})},"View in new visualization":function(){var o=i+"/trackster?"+$.param(k);n.frame_manager.frame_new({title:"Trackster",type:"url",content:o});n.hide_modal()}})}});return false}}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/mvc/tools.js
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var e={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var d=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new d(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:c},create:function(v){var w=d.TYPE_DICT[v.type]||d;return new w(v)}});var c=d.extend({defaults:t.extend({},d.prototype.defaults,{min:null,max:null}),initialize:function(){d.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return d.create(w)}))},urlRoot:galaxy_paths.get("tool_url"),copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,e);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var o=Backbone.Model.extend(e);var r=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof o){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(r.prototype,e);var b=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(b.prototype,e);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.type;if(z==="tool"){return v.attributes.tools.get(A.id)}else{if(z==="section"){var y=t.map(A.elems,x);A.elems=y;return new r(A)}else{if(z==="label"){return new o(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof r){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof o){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var f=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var i=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof o){var y=new f({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof r){var x=new i({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof o){var A=new f({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:d,IntegerToolParameter:c,Tool:h,ToolCollection:k,ToolSearch:b,ToolPanel:l,ToolPanelView:s,ToolFormView:q}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var e={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var d=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new d(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:c},create:function(v){var w=d.TYPE_DICT[v.type]||d;return new w(v)}});var c=d.extend({defaults:t.extend({},d.prototype.defaults,{min:null,max:null}),initialize:function(){d.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return d.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,e);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var o=Backbone.Model.extend(e);var r=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof o){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(r.prototype,e);var b=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(b.prototype,e);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.type;if(z==="tool"){return v.attributes.tools.get(A.id)}else{if(z==="section"){var y=t.map(A.elems,x);A.elems=y;return new r(A)}else{if(z==="label"){return new o(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof r){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof o){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var f=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var i=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof o){var y=new f({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof r){var x=new i({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof o){var A=new f({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:d,IntegerToolParameter:c,Tool:h,ToolCollection:k,ToolSearch:b,ToolPanel:l,ToolPanelView:s,ToolFormView:q}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/mvc/ui.js
--- a/static/scripts/packed/mvc/ui.js
+++ b/static/scripts/packed/mvc/ui.js
@@ -1,1 +1,1 @@
-var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.attributes);a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}if(b.title){a+=" tooltip"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false});this.$button.data("PopupMenu",this)},render:function(){var a=this;this.$el.addClass("popmenu-wrapper").css({position:"absolute",display:"none"});this.$el.html(this.template(this.$button.attr("id"),this.options));if(this.options.length){this.$el.find("li").each(function(c,b){var f=$(b),e=f.children("a.popupmenu-option"),d=a.options[c].func;if(e.length&&d){e.click(function(g){d(g,a.options[c])})}a.options[c].$li=f})}return this},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},_setUpCloseBehavior:function(){var b=this;var a=function(c){c.bind("click.close_popup",function(){b.remove();c.unbind("click.close_popup")})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"},template:function(e,b){var a='<ul id="'+e+'-menu" class="dropdown-menu">';if(b.length>0){for(var c in b){var d=b[c];if(d.divider){a+='<li class="divider"></li>'}else{if(d.header){a+='<li class="head"><a href="javascript:void(0);">'+d.html+"</a></li>"}else{if(d.href){a+='<li><a href="'+d.href+'"';a+='target="'+d.target+'"'}else{a+='<li><a href="javascript:void(0);"'}a+='class="popupmenu-option">';if(d.checked){a+='<span class="fa-icon-ok"></span>'}a+=d.html}}}}else{a+="<li>No Options.</li>"}return a+"</ul>"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(j){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}var i;switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;case"demo":if(i===undefined||i.closed){i=window.open(j,k);i.creator=self}break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};
\ No newline at end of file
+var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.attributes);a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}if(b.title){a+=" tooltip"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false});this.$button.data("PopupMenu",this)},render:function(){var a=this;this.$el.addClass("popmenu-wrapper").css({position:"absolute",display:"none"});this.$el.html(this.template(this.$button.attr("id"),this.options));if(this.options.length){this.$el.find("li").each(function(c,b){var f=$(b),e=f.children("a.popupmenu-option"),d=a.options[c].func;if(e.length&&d){e.click(function(g){d(g,a.options[c])})}a.options[c].$li=f})}return this},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},_setUpCloseBehavior:function(){var b=this;var a=function(c){c.bind("click.close_popup",function(){b.remove();c.unbind("click.close_popup")})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"},template:function(e,b){var a='<ul id="'+e+'-menu" class="dropdown-menu">';if(b.length>0){for(var c in b){var d=b[c];if(d.divider){a+='<li class="divider"></li>'}else{if(d.header){a+='<li class="head"><a href="javascript:void(0);">'+d.html+"</a></li>"}else{if(d.href){a+='<li><a href="'+d.href+'"';a+='target="'+d.target+'"'}else{a+='<li><a href="javascript:void(0);"'}a+='class="popupmenu-option">';if(d.checked){a+='<span class="fa-icon-ok"></span>'}a+=d.html}}}}else{a+="<li>No Options.</li>"}return a+"</ul>"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(j){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}var i;switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;case"demo":if(i===undefined||i.closed){i=window.open(j,k);i.creator=self}break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/mvc/visualizations/scatterplotControlForm.js
--- a/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js
+++ b/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js
@@ -1,1 +1,1 @@
-var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find(".tooltip").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]};
\ No newline at end of file
+var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_config.root+"static/images/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find(".tooltip").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]};
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/viz/circster.js
--- a/static/scripts/packed/viz/circster.js
+++ b/static/scripts/packed/viz/circster.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){if(n===undefined){n=2}if(o===null){return null}var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var x=new d({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(r[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(r[0])});var q=this.circular_views.length,n=new d({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});var e=Backbone.View.extend({initialize:function(){var n=new i.Genome(config.app.genome),o=new i.GenomeVisualization(config.app.viz_config),q=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.1,genome:n,model:o,dataset_arc_height:25});q.render();$("#center .unified-panel-header-inner").append(config.app.viz_config.title+" "+config.app.viz_config.dbkey);var p=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){i.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",o.get("dbkey"),function(r){o.add_tracks(r)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var r=config.app.viz_config;$.ajax({url:config.root+"visualization/save",type:"POST",dataType:"json",data:{id:r.vis_id,title:r.title,dbkey:r.dbkey,type:"trackster",vis_json:JSON.stringify(r)}}).success(function(s){hide_modal();r.vis_id=s.vis_id;r.has_changes=false;window.history.pushState({},"",s.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});p.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(p.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}});
\ No newline at end of file
+define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){if(n===undefined){n=2}if(o===null){return null}var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var x=new d({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(r[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(r[0])});var q=this.circular_views.length,n=new d({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});var e=Backbone.View.extend({initialize:function(){var n=new i.Genome(galaxy_config.app.genome),o=new i.GenomeVisualization(galaxy_config.app.viz_config),q=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.1,genome:n,model:o,dataset_arc_height:25});q.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var p=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){i.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",o.get("dbkey"),function(r){o.add_tracks(r)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var r=galaxy_config.app.viz_config;$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:r.vis_id,title:r.title,dbkey:r.dbkey,type:"trackster",vis_json:JSON.stringify(r)}}).success(function(s){hide_modal();r.vis_id=s.vis_id;r.has_changes=false;window.history.pushState({},"",s.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});p.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(p.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/viz/trackster.js
--- a/static/scripts/packed/viz/trackster.js
+++ b/static/scripts/packed/viz/trackster.js
@@ -1,1 +1,1 @@
-var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/jquery-ui-combobox","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("/static/style/jquery.rating.css");a.load_file("/static/style/history.css");a.load_file("/static/style/autocomplete_tagging.css");a.load_file("/static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("/static/style/library.css");a.load_file("/static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){show_modal("New Visualization",e.template_view_new(f),{Cancel:function(){window.location=config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val())}});if(config.app.default_dbkey){$("#new-dbkey option[value='"+config.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").combobox({appendTo:$("#overlay"),size:40});$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},config.app.gene_region);this.init_editor();view.editor=true;hide_modal()},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(config.app.add_dataset){$.ajax({url:config.root+"api/datasets/"+config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}});
\ No newline at end of file
+var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/jquery-ui-combobox","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("/static/style/jquery.rating.css");a.load_file("/static/style/history.css");a.load_file("/static/style/autocomplete_tagging.css");a.load_file("/static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("/static/style/library.css");a.load_file("/static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){show_modal("New Visualization",e.template_view_new(f),{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val())}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").combobox({appendTo:$("#overlay"),size:40});$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true;hide_modal()},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/viz/trackster/tracks.js
--- a/static/scripts/packed/viz/trackster/tracks.js
+++ b/static/scripts/packed/viz/trackster/tracks.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}]});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=Backbone.RelationalModel.extend({defaults:{track:null,tool:null,},relations:[{type:Backbone.HasOne,key:"tool",relatedModel:R.Tool}]});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},state_dict:function(){var ad=this.model.get("tool").get_param_values_dict();ad.visible=this.parent_div.is(":visible");return ad},run_on_dataset:function(){var ad=this.model.get("tool");this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model.get("tool"),aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get("tool").get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".bs-tooltip").removeClass("in");var ax=$(this).siblings(".bs-tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/viz/trackster_ui.js
--- a/static/scripts/packed/viz/trackster_ui.js
+++ b/static/scripts/packed/viz/trackster_ui.js
@@ -1,1 +1,1 @@
-define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(config.root+"visualization/list_current_history_datasets",config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){hide_modal();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){show_modal("Select dataset for new bookmarks",m,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});hide_modal()}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}});
\ No newline at end of file
+define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){hide_modal();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){show_modal("Select dataset for new bookmarks",m,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});hide_modal()}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/packed/viz/visualization.js
--- a/static/scripts/packed/viz/visualization.js
+++ b/static/scripts/packed/viz/visualization.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("promise" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_paths.attributes.image_path+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=w.toString(),u=s.indexOf(y,function(z){return z.toString()===v});if(u!==-1){if(x[v].stale){y.splice(u,1);delete x[v]}else{this.move_key_to_end(w,u)}}return x[v]},set_elt:function(w,y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,v=w.toString(),x=this.attributes.num_elements;if(!z[v]){if(A.length>=x){var u=A.shift();delete z[u.toString()]}A.push(w)}z[v]=y;return y},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),u=this.get("obj_cache"),v,z;for(var x=0;x<D.length;x++){v=D[x];if(v.contains(B)){z=true;C=u[v.toString()];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(v,x);if(!j(C)){var F=this.subset_entry(C,B);this.set(B,F);C=F}return C}}}if(!z&&B.length()<this.attributes.min_region_size){var E=this.most_recently_added();if(!E||(B.get("start")>E.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=Backbone.RelationalModel.extend({relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:i.Dataset}],initialize:function(u){this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}});
\ No newline at end of file
+define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("promise" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_config.root+"static/images"+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=w.toString(),u=s.indexOf(y,function(z){return z.toString()===v});if(u!==-1){if(x[v].stale){y.splice(u,1);delete x[v]}else{this.move_key_to_end(w,u)}}return x[v]},set_elt:function(w,y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,v=w.toString(),x=this.attributes.num_elements;if(!z[v]){if(A.length>=x){var u=A.shift();delete z[u.toString()]}A.push(w)}z[v]=y;return y},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),u=this.get("obj_cache"),v,z;for(var x=0;x<D.length;x++){v=D[x];if(v.contains(B)){z=true;C=u[v.toString()];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(v,x);if(!j(C)){var F=this.subset_entry(C,B);this.set(B,F);C=F}return C}}}if(!z&&B.length()<this.attributes.min_region_size){var E=this.most_recently_added();if(!E||(B.get("start")>E.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=Backbone.RelationalModel.extend({relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:i.Dataset}],initialize:function(u){this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}});
\ No newline at end of file
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/viz/circster.js
--- a/static/scripts/viz/circster.js
+++ b/static/scripts/viz/circster.js
@@ -960,8 +960,8 @@
initialize: function ()
{
// configure visualization
- var genome = new visualization.Genome(config.app.genome),
- vis = new visualization.GenomeVisualization(config.app.viz_config),
+ var genome = new visualization.Genome(galaxy_config.app.genome),
+ vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config),
viz_view = new CircsterView(
{
// view pane
@@ -978,13 +978,13 @@
viz_view.render();
// setup title
- $('#center .unified-panel-header-inner').append(config.app.viz_config.title + " " + config.app.viz_config.dbkey);
+ $('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + " " + galaxy_config.app.viz_config.dbkey);
// setup menu
var menu = create_icon_buttons_menu([
{ icon_class: 'plus-button', title: 'Add tracks', on_click: function()
{
- visualization.select_datasets(config.root + "visualization/list_current_history_datasets", config.root + "api/datasets", vis.get('dbkey'), function(tracks)
+ visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", vis.get('dbkey'), function(tracks)
{
vis.add_tracks(tracks);
});
@@ -996,11 +996,11 @@
show_modal("Saving...", "progress");
// link configuration
- var view = config.app.viz_config;
+ var view = galaxy_config.app.viz_config;
// send to server
$.ajax({
- url: config.root + "visualization/save",
+ url: galaxy_config.root + "visualization/save",
type: "POST",
dataType: "json",
data: {
@@ -1025,7 +1025,7 @@
},{
icon_class: 'cross-circle', title: 'Close', on_click: function()
{
- window.location = config.root + "visualization/list";
+ window.location = galaxy_config.root + "visualization/list";
}
}], { tooltip_config: { placement: 'bottom' } });
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -40,7 +40,7 @@
initialize : function ()
{
// load ui
- ui = new trackster_ui.TracksterUI(config.root);
+ ui = new trackster_ui.TracksterUI(galaxy_config.root);
// create button menu
ui.createButtonMenu();
@@ -62,7 +62,7 @@
force_right_panel("hide");
// check if id is available
- if (config.app.id)
+ if (galaxy_config.app.id)
this.view_existing();
else
this.view_new();
@@ -79,7 +79,7 @@
view_existing : function ()
{
// get config
- var viz_config = config.app.viz_config;
+ var viz_config = galaxy_config.app.viz_config;
// view
view = ui.create_visualization(
@@ -98,9 +98,9 @@
view_new : function ()
{
// availability of default database key
- /*if (config.app.default_dbkey !== undefined)
+ /*if (galaxy_config.app.default_dbkey !== undefined)
{
- this.create_browser("Unnamed", config.app.default_dbkey);
+ this.create_browser("Unnamed", galaxy_config.app.default_dbkey);
return;
}*/
@@ -110,7 +110,7 @@
// ajax
$.ajax(
{
- url: config.root + "api/genomes?chrom_info=True",
+ url: galaxy_config.root + "api/genomes?chrom_info=True",
data: {},
error: function() { alert( "Couldn't create new browser." ); },
success: function(response)
@@ -118,13 +118,13 @@
// show dialog
show_modal("New Visualization", self.template_view_new(response),
{
- "Cancel": function() { window.location = config.root + "visualization/list"; },
+ "Cancel": function() { window.location = galaxy_config.root + "visualization/list"; },
"Create": function() { self.create_browser($("#new-title").val(), $("#new-dbkey").val()); }
});
// select default
- if (config.app.default_dbkey)
- $("#new-dbkey option[value='" + config.default_dbkey +"']").attr("selected", true);
+ if (galaxy_config.app.default_dbkey)
+ $("#new-dbkey option[value='" + galaxy_config.app.default_dbkey + "']").attr("selected", true);
// change focus
$("#new-title").focus();
@@ -168,7 +168,7 @@
'</div>' +
'<div class="form-row">' +
'Is the build not listed here? ' +
- '<a href="' + config.root + 'user/dbkeys?use_panels=True">Add a Custom Build</a>' +
+ '<a href="' + galaxy_config.root + 'user/dbkeys?use_panels=True">Add a Custom Build</a>' +
'</div>' +
'</form>';
@@ -186,7 +186,7 @@
container: $("#center .unified-panel-body"),
name: name,
dbkey: dbkey
- }, config.app.gene_region);
+ }, galaxy_config.app.gene_region);
// initialize editor
this.init_editor();
@@ -205,9 +205,9 @@
$("#center .unified-panel-title").text(view.name + " (" + view.dbkey + ")");
// add dataset
- if (config.app.add_dataset)
+ if (galaxy_config.app.add_dataset)
$.ajax({
- url: config.root + "api/datasets/" + config.app.add_dataset,
+ url: galaxy_config.root + "api/datasets/" + galaxy_config.app.add_dataset,
data: { hda_ldda: 'hda', data_type: 'track_config' },
dataType: "json",
success: function(track_data) { view.add_drawable( trackster_ui.object_from_template(track_data, view, view) ); }
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -951,7 +951,7 @@
// Introduction div shown when there are no tracks.
this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide();
var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () {
- visualization.select_datasets(config.root + "visualization/list_current_history_datasets", config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
+ visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
_.each(tracks, function(track) {
view.add_drawable( object_from_template(track, view, view) );
});
@@ -1219,7 +1219,7 @@
view = this,
chrom_data = $.Deferred();
$.ajax({
- url: config.root + "api/genomes/" + this.dbkey,
+ url: galaxy_config.root + "api/genomes/" + this.dbkey,
data: url_parms,
dataType: "json",
success: function (result) {
@@ -1846,7 +1846,7 @@
url_params.inputs = this.model.get('tool').get_inputs_dict();
var ss_deferred = new util.ServerStateDeferred({
ajax_settings: {
- url: config.root + "api/tools",
+ url: galaxy_config.root + "api/tools",
data: JSON.stringify(url_params),
dataType: "json",
contentType: 'application/json',
@@ -2453,7 +2453,7 @@
// Go to visualization.
window.location.href =
- config.root + "visualization/sweepster" + "?" +
+ galaxy_config.root + "visualization/sweepster" + "?" +
$.param({
dataset_id: track.dataset.id,
hda_ldda: track.dataset.get('hda_ldda'),
@@ -3728,7 +3728,7 @@
this.content_div.css("background", "none");
this.content_div.css("min-height", "0px");
this.content_div.css("border", "none");
- this.data_url = config.root + "api/genomes/" + "/" + this.view.dbkey;
+ this.data_url = galaxy_config.root + "api/genomes/" + "/" + this.view.dbkey;
this.data_url_extra_params = {reference: true};
this.data_manager = new visualization.GenomeReferenceDataManager({
data_url: this.data_url,
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/viz/trackster_ui.js
--- a/static/scripts/viz/trackster_ui.js
+++ b/static/scripts/viz/trackster_ui.js
@@ -41,7 +41,7 @@
var self = this,
menu = create_icon_buttons_menu([
{ icon_class: 'plus-button', title: 'Add tracks', on_click: function() {
- visualization.select_datasets(config.root + "visualization/list_current_history_datasets", config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
+ visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
_.each(tracks, function(track) {
view.add_drawable( object_from_template(track, view, view) );
});
@@ -83,7 +83,7 @@
};
$.ajax({
- url: config.root + "visualization/save",
+ url: galaxy_config.root + "visualization/save",
type: "POST",
dataType: "json",
data: {
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -100,7 +100,7 @@
var patterns = this.patterns,
dummy_context = this.dummy_context,
image = new Image();
- image.src = galaxy_paths.attributes.image_path + path;
+ image.src = galaxy_config.root + "static/images" + path;
image.onload = function() {
patterns[key] = dummy_context.createPattern( image, "repeat" );
};
@@ -914,7 +914,7 @@
},
// No API to create/save visualization yet, so use this path:
- url: galaxy_paths.get("visualization_url"),
+ url: galaxy_config.root + "visualization/save",
/**
* POSTs visualization's JSON to its URL using the parameter 'vis_json'
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 templates/base.mako
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -57,6 +57,12 @@
)}
<script type="text/javascript">
+ ## global configuration object
+ var galaxy_config =
+ {
+ root: '${h.url_for( "/" )}'
+ };
+
// console protection
window.console = window.console || {
log : function(){},
@@ -66,12 +72,6 @@
error : function(){},
assert : function(){}
};
-
- // Set up needed paths.
- var galaxy_paths = new GalaxyPaths({
- root_path: '${h.url_for( "/" )}',
- image_path: '${h.url_for( "/static/images" )}'
- });
</script>
%if not form_input_auto_focus is UNDEFINED and form_input_auto_focus:
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 templates/base/base_panels.mako
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -71,16 +71,15 @@
)}
<script type="text/javascript">
- ## path to style sheets
- var galaxy_config = {
- url: {
- styles : "${h.url_for('/static/style')}"
- }
+ ## global configuration object
+ var galaxy_config =
+ {
+ root: '${h.url_for( "/" )}'
};
## load additional style sheet
if (window != window.top)
- $('<link href="' + galaxy_config.url.styles + '/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head');
+ $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head');
// console protection
window.console = window.console || {
@@ -92,19 +91,6 @@
assert : function(){}
};
- // Set up needed paths.
- var galaxy_paths = new GalaxyPaths({
- root_path: '${h.url_for( "/" )}',
- image_path: '${h.url_for( "/static/images" )}',
-
- tool_url: '${h.url_for( controller="/api/tools" )}',
- history_url: '${h.url_for( controller="/api/histories" )}',
-
- datasets_url: '${h.url_for( controller="/api/datasets" )}',
- sweepster_url: '${h.url_for( controller="/visualization", action="sweepster" )}',
- visualization_url: '${h.url_for( controller="/visualization", action="save" )}',
- });
-
## configure require
require.config({
baseUrl: "${h.url_for('/static/scripts') }",
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 templates/webapps/galaxy/galaxy.masthead.mako
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -29,16 +29,9 @@
<%def name="load()">
## load the frame manager
<script type="text/javascript">
- ## path to style sheets
- var galaxy_config = {
- url: {
- styles : "${h.url_for('/static/style')}"
- }
- };
-
## load additional style sheet
if (window != window.top)
- $('<link href="' + galaxy_config.url.styles + '/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head');
+ $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head');
## frame manager
var frame_manager = null;
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 templates/webapps/galaxy/galaxy.panels.mako
--- a/templates/webapps/galaxy/galaxy.panels.mako
+++ b/templates/webapps/galaxy/galaxy.panels.mako
@@ -68,13 +68,6 @@
error : function(){},
assert : function(){}
};
-
- // set up needed paths
- var galaxy_paths = new GalaxyPaths({
- image_path: '${h.url_for( "/static/images" )}',
- datasets_url: '${h.url_for( controller="/api/datasets" )}',
- visualization_url: '${h.url_for( controller="/visualization", action="save" )}',
- });
</script>
## load default style
@@ -112,13 +105,13 @@
});
## get configuration
- var config = ${ h.to_json_string( self.galaxy_config ) };
+ var galaxy_config = ${ h.to_json_string( self.galaxy_config ) };
## on page load
$(function()
{
## check if script is defined
- var jscript = config.app.jscript;
+ var jscript = galaxy_config.app.jscript;
if (jscript)
{
## load galaxy app
@@ -128,7 +121,7 @@
var module = new js_lib.GalaxyApp();
});
} else
- console.log("'config.app.jscript' missing.");
+ console.log("'galaxy_config.app.jscript' missing.");
});
</script></%def>
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 templates/webapps/galaxy/root/history.mako
--- a/templates/webapps/galaxy/root/history.mako
+++ b/templates/webapps/galaxy/root/history.mako
@@ -204,10 +204,9 @@
// set js localizable strings
GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } );
-// add needed controller urls to GalaxyPaths
-if( !galaxy_paths ){ galaxy_paths = top.galaxy_paths || new GalaxyPaths(); }
-galaxy_paths.set( 'hda', ${get_hda_url_templates()} );
-galaxy_paths.set( 'history', ${get_history_url_templates()} );
+// add needed controller urls to galaxy_config
+galaxy_config['hda'] = ${get_hda_url_templates()};
+galaxy_config['history'] = ${get_history_url_templates()};
$(function(){
galaxyPageSetUp();
@@ -247,7 +246,7 @@
var history = new History( historyJson, hdaJson, ( debugging )?( console ):( null ) );
var historyPanel = new HistoryPanel({
model : history,
- urlTemplates : galaxy_paths.attributes,
+ urlTemplates : galaxy_config,
logger : ( debugging )?( console ):( null ),
// is page sending in show settings? if so override history's
show_deleted : page_show_deleted,
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 templates/webapps/galaxy/visualization/display.mako
--- a/templates/webapps/galaxy/visualization/display.mako
+++ b/templates/webapps/galaxy/visualization/display.mako
@@ -65,19 +65,11 @@
require( ["base", "viz/visualization", "viz/trackster_ui", "viz/trackster/tracks"],
function( base, visualization, trackster_ui, tracks ) {
- ${render_trackster_js_vars()}
-
// FIXME: deliberate global required for now due to requireJS integration.
view = null;
var ui = new (trackster_ui.TracksterUI)( "${h.url_for('/')}" )
container_element = $("#${trans.security.encode_id( visualization.id )}");
-
- // global config
- config =
- {
- 'root' : '${h.url_for("/")}'
- };
$(function() {
var is_embedded = (container_element.parents(".item-content").length > 0);
diff -r 4f4e01316260d300dc10da137cbbd5905114b7f5 -r 3a1f4df1591c28287d9fb1c8efc4e7321e0dde70 templates/webapps/galaxy/visualization/trackster_common.mako
--- a/templates/webapps/galaxy/visualization/trackster_common.mako
+++ b/templates/webapps/galaxy/visualization/trackster_common.mako
@@ -13,13 +13,4 @@
<%def name="render_trackster_js_files()">
${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui", "libs/jquery/jquery-ui-combobox",
"libs/require", "libs/farbtastic" )}
-</%def>
-
-## Render a block of JavaScript that contains all necessary variables for Trackster.
-<%def name="render_trackster_js_vars()">
- add_track_async_url = "${h.url_for( controller='/api/datasets' )}";
- select_datasets_url = "${h.url_for( controller='/visualization', action='list_current_history_datasets' )}";
- reference_url = "${h.url_for( controller='/api/genomes' )}";
- chrom_url = "${h.url_for( controller='/api/genomes' )}";
- datasets_url = "${h.url_for( controller='/api/datasets' )}";
</%def>
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Rename APIItem mixin to DictifiableMixin and rename associated attributes and functions as well. Renaming was done because dictification is needed in many places throughout Galaxy, not just the API.
by commits-noreplyï¼ bitbucket.org 21 Aug '13
by commits-noreplyï¼ bitbucket.org 21 Aug '13
21 Aug '13
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4f4e01316260/
Changeset: 4f4e01316260
User: jgoecks
Date: 2013-08-20 21:43:38
Summary: Rename APIItem mixin to DictifiableMixin and rename associated attributes and functions as well. Renaming was done because dictification is needed in many places throughout Galaxy, not just the API.
Affected #: 35 files
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 config/plugins/visualizations/scatterplot/templates/scatterplot.mako
--- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako
+++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako
@@ -41,7 +41,7 @@
<script type="text/javascript">
$(function(){
- var hda = ${h.to_json_string( trans.security.encode_dict_ids( hda.get_api_value() ) )},
+ var hda = ${h.to_json_string( trans.security.encode_dict_ids( hda.dictify() ) )},
querySettings = ${h.to_json_string( query_args )},
chartConfig = _.extend( querySettings, {
containerSelector : '#chart',
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -23,7 +23,7 @@
import galaxy.datatypes.registry
import galaxy.security.passwords
from galaxy.datatypes.metadata import MetadataCollection
-from galaxy.model.item_attrs import APIItem, UsesAnnotations
+from galaxy.model.item_attrs import DictifiableMixin, UsesAnnotations
from galaxy.security import get_permitted_actions
from galaxy.util import is_multi_byte, nice_size, Params, restore_text, send_mail
from galaxy.util.bunch import Bunch
@@ -61,16 +61,16 @@
datatypes_registry = d_registry
-class User( object, APIItem ):
+class User( object, DictifiableMixin ):
use_pbkdf2 = True
"""
Data for a Galaxy user or admin and relations to their
histories, credentials, and roles.
"""
- # attributes that will be accessed and returned when calling get_api_value( view='collection' )
- api_collection_visible_keys = ( 'id', 'email' )
- # attributes that will be accessed and returned when calling get_api_value( view='element' )
- api_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' )
+ # attributes that will be accessed and returned when calling dictify( view='collection' )
+ dict_collection_visible_keys = ( 'id', 'email' )
+ # attributes that will be accessed and returned when calling dictify( view='element' )
+ dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' )
def __init__( self, email=None, password=None ):
self.email = email
@@ -157,9 +157,9 @@
return total
-class Job( object, APIItem ):
- api_collection_visible_keys = [ 'id' ]
- api_element_visible_keys = [ 'id' ]
+class Job( object, DictifiableMixin ):
+ dict_collection_visible_keys = [ 'id' ]
+ dict_element_visible_keys = [ 'id' ]
"""
A job represents a request to run a tool given input datasets, tool
@@ -363,8 +363,8 @@
dataset.blurb = 'deleted'
dataset.peek = 'Job deleted'
dataset.info = 'Job output deleted by user before job completed'
- def get_api_value( self, view='collection' ):
- rval = super( Job, self ).get_api_value( view=view )
+ def dictify( self, view='collection' ):
+ rval = super( Job, self ).dictify( view=view )
rval['tool_name'] = self.tool_id
param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] )
rval['params'] = param_dict
@@ -649,9 +649,9 @@
else:
return False
-class Group( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name' )
- api_element_visible_keys = ( 'id', 'name' )
+class Group( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name' )
+ dict_element_visible_keys = ( 'id', 'name' )
def __init__( self, name = None ):
self.name = name
@@ -662,10 +662,10 @@
self.user = user
self.group = group
-class History( object, APIItem, UsesAnnotations ):
+class History( object, DictifiableMixin, UsesAnnotations ):
- api_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' )
- api_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged' )
+ dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' )
+ dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged' )
default_name = 'Unnamed history'
def __init__( self, id=None, name=None, user=None ):
@@ -780,10 +780,10 @@
history_name = unicode(history_name, 'utf-8')
return history_name
- def get_api_value( self, view='collection', value_mapper = None ):
+ def dictify( self, view='collection', value_mapper = None ):
# Get basic value.
- rval = super( History, self ).get_api_value( view=view, value_mapper=value_mapper )
+ rval = super( History, self ).dictify( view=view, value_mapper=value_mapper )
# Add tags.
tags_str_list = []
@@ -800,14 +800,14 @@
#AKA: set_api_value
"""
Set object attributes to the values in dictionary new_data limiting
- to only those keys in api_element_visible_keys.
+ to only those keys in dict_element_visible_keys.
Returns a dictionary of the keys, values that have been changed.
"""
# precondition: keys are proper, values are parsed and validated
changed = {}
# unknown keys are ignored here
- for key in [ k for k in new_data.keys() if k in self.api_element_visible_keys ]:
+ for key in [ k for k in new_data.keys() if k in self.dict_element_visible_keys ]:
new_val = new_data[ key ]
old_val = self.__getattribute__( key )
if new_val == old_val:
@@ -869,9 +869,9 @@
self.group = group
self.role = role
-class Role( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name' )
- api_element_visible_keys = ( 'id', 'name', 'description', 'type' )
+class Role( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name' )
+ dict_element_visible_keys = ( 'id', 'name', 'description', 'type' )
private_id = None
types = Bunch(
PRIVATE = 'private',
@@ -886,21 +886,21 @@
self.type = type
self.deleted = deleted
-class UserQuotaAssociation( object, APIItem ):
- api_element_visible_keys = ( 'user', )
+class UserQuotaAssociation( object, DictifiableMixin ):
+ dict_element_visible_keys = ( 'user', )
def __init__( self, user, quota ):
self.user = user
self.quota = quota
-class GroupQuotaAssociation( object, APIItem ):
- api_element_visible_keys = ( 'group', )
+class GroupQuotaAssociation( object, DictifiableMixin ):
+ dict_element_visible_keys = ( 'group', )
def __init__( self, group, quota ):
self.group = group
self.quota = quota
-class Quota( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name' )
- api_element_visible_keys = ( 'id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups' )
+class Quota( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name' )
+ dict_element_visible_keys = ( 'id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups' )
valid_operations = ( '+', '-', '=' )
def __init__( self, name="", description="", amount=0, operation="=" ):
self.name = name
@@ -927,8 +927,8 @@
else:
return nice_size( self.bytes )
-class DefaultQuotaAssociation( Quota, APIItem ):
- api_element_visible_keys = ( 'type', )
+class DefaultQuotaAssociation( Quota, DictifiableMixin ):
+ dict_element_visible_keys = ( 'type', )
types = Bunch(
UNREGISTERED = 'unregistered',
REGISTERED = 'registered'
@@ -1680,7 +1680,7 @@
rval += child.get_disk_usage( user )
return rval
- def get_api_value( self, view='collection' ):
+ def dictify( self, view='collection' ):
"""
Return attributes of this HDA that are exposed using the API.
"""
@@ -1759,10 +1759,10 @@
self.subset = subset
self.location = location
-class Library( object, APIItem ):
+class Library( object, DictifiableMixin ):
permitted_actions = get_permitted_actions( filter='LIBRARY' )
- api_collection_visible_keys = ( 'id', 'name' )
- api_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' )
+ dict_collection_visible_keys = ( 'id', 'name' )
+ dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' )
def __init__( self, name=None, description=None, synopsis=None, root_folder=None ):
self.name = name or "Unnamed library"
self.description = description
@@ -1828,8 +1828,8 @@
name = unicode( name, 'utf-8' )
return name
-class LibraryFolder( object, APIItem ):
- api_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' )
+class LibraryFolder( object, DictifiableMixin ):
+ dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' )
def __init__( self, name=None, description=None, item_count=0, order_id=None ):
self.name = name or "Unnamed folder"
self.description = description
@@ -1900,8 +1900,8 @@
if isinstance( name, str ):
name = unicode( name, 'utf-8' )
return name
- def get_api_value( self, view='collection' ):
- rval = super( LibraryFolder, self ).get_api_value( view=view )
+ def dictify( self, view='collection' ):
+ rval = super( LibraryFolder, self ).dictify( view=view )
info_association, inherited = self.get_info_association()
if info_association:
if inherited:
@@ -1966,7 +1966,7 @@
name = property( get_name, set_name )
def display_name( self ):
self.library_dataset_dataset_association.display_name()
- def get_api_value( self, view='collection' ):
+ def dictify( self, view='collection' ):
# Since this class is a proxy to rather complex attributes we want to
# display in other objects, we can't use the simpler method used by
# other model classes.
@@ -2096,7 +2096,7 @@
if restrict:
return None, inherited
return self.library_dataset.folder.get_info_association( inherited=True )
- def get_api_value( self, view='collection' ):
+ def dictify( self, view='collection' ):
# Since this class is a proxy to rather complex attributes we want to
# display in other objects, we can't use the simpler method used by
# other model classes.
@@ -2323,9 +2323,9 @@
self.id = None
self.user = None
-class StoredWorkflow( object, APIItem):
- api_collection_visible_keys = ( 'id', 'name', 'published' )
- api_element_visible_keys = ( 'id', 'name', 'published' )
+class StoredWorkflow( object, DictifiableMixin):
+ dict_collection_visible_keys = ( 'id', 'name', 'published' )
+ dict_element_visible_keys = ( 'id', 'name', 'published' )
def __init__( self ):
self.id = None
self.user = None
@@ -2341,8 +2341,8 @@
new_swta.user = target_user
self.tags.append(new_swta)
- def get_api_value( self, view='collection', value_mapper = None ):
- rval = APIItem.get_api_value(self, view=view, value_mapper = value_mapper)
+ def dictify( self, view='collection', value_mapper = None ):
+ rval = DictifiableMixin.dictify(self, view=view, value_mapper = value_mapper)
tags_str_list = []
for tag in self.tags:
tag_str = tag.user_tname
@@ -2434,7 +2434,7 @@
return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
-class FormDefinition( object, APIItem ):
+class FormDefinition( object, DictifiableMixin ):
# The following form_builder classes are supported by the FormDefinition class.
supported_field_types = [ AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField ]
types = Bunch( REQUEST = 'Sequencing Request Form',
@@ -2443,8 +2443,8 @@
RUN_DETAILS_TEMPLATE = 'Sample run details template',
LIBRARY_INFO_TEMPLATE = 'Library information template',
USER_INFO = 'User Information' )
- api_collection_visible_keys = ( 'id', 'name' )
- api_element_visible_keys = ( 'id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout' )
+ dict_collection_visible_keys = ( 'id', 'name' )
+ dict_element_visible_keys = ( 'id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout' )
def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ):
self.name = name
self.desc = desc
@@ -2562,12 +2562,12 @@
self.form_definition = form_def
self.content = content
-class Request( object, APIItem ):
+class Request( object, DictifiableMixin ):
states = Bunch( NEW = 'New',
SUBMITTED = 'In Progress',
REJECTED = 'Rejected',
COMPLETE = 'Complete' )
- api_collection_visible_keys = ( 'id', 'name', 'state' )
+ dict_collection_visible_keys = ( 'id', 'name', 'state' )
def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ):
self.name = name
self.desc = desc
@@ -2753,9 +2753,9 @@
def populate_actions( self, trans, item, param_dict=None ):
return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict )
-class RequestType( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name', 'desc' )
- api_element_visible_keys = ( 'id', 'name', 'desc', 'request_form_id', 'sample_form_id' )
+class RequestType( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name', 'desc' )
+ dict_element_visible_keys = ( 'id', 'name', 'desc', 'request_form_id', 'sample_form_id' )
rename_dataset_options = Bunch( NO = 'Do not rename',
SAMPLE_NAME = 'Preprend sample name',
EXPERIMENT_NAME = 'Prepend experiment name',
@@ -2839,12 +2839,12 @@
self.request_type = request_type
self.role = role
-class Sample( object, APIItem ):
+class Sample( object, DictifiableMixin ):
# The following form_builder classes are supported by the Sample class.
supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ]
bulk_operations = Bunch( CHANGE_STATE = 'Change state',
SELECT_LIBRARY = 'Select data library and folder' )
- api_collection_visible_keys = ( 'id', 'name' )
+ dict_collection_visible_keys = ( 'id', 'name' )
def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None):
self.name = name
self.desc = desc
@@ -3169,9 +3169,9 @@
def __str__ ( self ):
return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name )
-class ItemTagAssociation ( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'user_tname', 'user_value' )
- api_element_visible_keys = api_collection_visible_keys
+class ItemTagAssociation ( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'user_tname', 'user_value' )
+ dict_element_visible_keys = dict_collection_visible_keys
def __init__( self, id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None ):
self.id = id
@@ -3307,9 +3307,9 @@
pass
class ToolShedRepository( object ):
- api_collection_visible_keys = ( 'id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
+ dict_collection_visible_keys = ( 'id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
'update_available', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message' )
- api_element_visible_keys = ( 'id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
+ dict_element_visible_keys = ( 'id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
'update_available', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message' )
installation_status = Bunch( NEW='New',
CLONING='Cloning',
@@ -3347,7 +3347,7 @@
self.status = status
self.error_message = error_message
def as_dict( self, value_mapper=None ):
- return self.get_api_value( view='element', value_mapper=value_mapper )
+ return self.dictify( view='element', value_mapper=value_mapper )
def repo_files_directory( self, app ):
repo_path = self.repo_path( app )
if repo_path:
@@ -3435,7 +3435,7 @@
if self.shed_config_filename == shed_tool_conf_dict[ 'config_filename' ]:
return shed_tool_conf_dict
return default
- def get_api_value( self, view='collection', value_mapper=None ):
+ def dictify( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -3699,8 +3699,8 @@
self.tool_shed_repository.name,
self.tool_shed_repository.installed_changeset_revision )
-class ToolVersion( object, APIItem ):
- api_element_visible_keys = ( 'id', 'tool_shed_repository' )
+class ToolVersion( object, DictifiableMixin ):
+ dict_element_visible_keys = ( 'id', 'tool_shed_repository' )
def __init__( self, id=None, create_time=None, tool_id=None, tool_shed_repository=None ):
self.id = id
self.create_time = create_time
@@ -3757,8 +3757,8 @@
return version_ids
return [ tool_version.tool_id for tool_version in self.get_versions( app ) ]
- def get_api_value( self, view='element' ):
- rval = APIItem.get_api_value(self, view)
+ def dictify( self, view='element' ):
+ rval = DictifiableMixin.dictify(self, view)
rval['tool_name'] = self.tool_id
for a in self.parent_tool_association:
rval['parent_tool_id'] = a.parent_id
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/model/item_attrs.py
--- a/lib/galaxy/model/item_attrs.py
+++ b/lib/galaxy/model/item_attrs.py
@@ -158,10 +158,12 @@
class_name = '%sAnnotationAssociation' % item.__class__.__name__
return getattr( galaxy.model, class_name, None )
-class APIItem:
- """ Mixin for api representation. """
+class DictifiableMixin:
+ """ Mixin that enables objects to be converted to dictionaries. This is useful
+ when for sharing objects across boundaries, such as the API, tool scripts,
+ and JavaScript code. """
- def get_api_value( self, view='collection', value_mapper=None ):
+ def dictify( self, view='collection', value_mapper=None ):
"""
Return item dictionary.
"""
@@ -174,9 +176,9 @@
Recursive helper function to get item values.
"""
# FIXME: why use exception here? Why not look for key in value_mapper
- # first and then default to get_api_value?
+ # first and then default to dictify?
try:
- return item.get_api_value( view=view, value_mapper=value_mapper )
+ return item.dictify( view=view, value_mapper=value_mapper )
except:
if key in value_mapper:
return value_mapper.get( key )( item )
@@ -189,7 +191,7 @@
# Fill item dict with visible keys.
try:
- visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' )
+ visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' )
except AttributeError:
raise Exception( 'Unknown API view: %s' % view )
for key in visible_keys:
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/model/search.py
--- a/lib/galaxy/model/search.py
+++ b/lib/galaxy/model/search.py
@@ -560,7 +560,7 @@
return self.view.get_results(True)
def item_to_api_value(self, item):
- r = item.get_api_value( view='element' )
+ r = item.dictify( view='element' )
if self.query.field_list.count("*"):
return r
o = {}
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -422,7 +422,7 @@
def get_history_dict( self, trans, history, hda_dictionaries=None ):
"""Returns history data in the form of a dictionary.
"""
- history_dict = history.get_api_value( view='element', value_mapper={ 'id':trans.security.encode_id })
+ history_dict = history.dictify( view='element', value_mapper={ 'id':trans.security.encode_id })
history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True )
history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, history )
@@ -583,7 +583,7 @@
"""
#precondition: the user's access to this hda has already been checked
#TODO:?? postcondition: all ids are encoded (is this really what we want at this level?)
- hda_dict = hda.get_api_value( view='element' )
+ hda_dict = hda.dictify( view='element' )
hda_dict[ 'api_type' ] = "file"
# Add additional attributes that depend on trans can hence must be added here rather than at the model level.
@@ -594,7 +594,7 @@
# ---- return here if deleted AND purged OR can't access
purged = ( hda.purged or hda.dataset.purged )
if ( hda.deleted and purged ):
- #TODO: get_api_value should really go AFTER this - only summary data
+ #TODO: dictify should really go AFTER this - only summary data
return trans.security.encode_dict_ids( hda_dict )
if trans.user_is_admin() or trans.app.config.expose_dataset_path:
@@ -911,7 +911,7 @@
return query
return query.all()
- #TODO: move into model (get_api_value)
+ #TODO: move into model (dictify)
def get_visualization_summary_dict( self, visualization ):
"""
Return a set of summary attributes for a visualization in dictionary form.
@@ -1132,7 +1132,7 @@
source='data' )
return {
"track_type": dataset.datatype.track_type,
- "dataset": trans.security.encode_dict_ids( dataset.get_api_value() ),
+ "dataset": trans.security.encode_dict_ids( dataset.dictify() ),
"name": track_dict['name'],
"prefs": prefs,
"mode": track_dict.get( 'mode', 'Auto' ),
@@ -1212,7 +1212,7 @@
return {
"track_type": dataset.datatype.track_type,
"name": dataset.name,
- "dataset": trans.security.encode_dict_ids( dataset.get_api_value() ),
+ "dataset": trans.security.encode_dict_ids( dataset.dictify() ),
"prefs": {},
"filters": { 'filters' : track_data_provider.get_filters() },
"tool": get_tool_def( trans, dataset ),
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/datasets.py
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -60,7 +60,7 @@
rval[ 'display_types' ] = self.get_old_display_applications( trans, dataset )
rval[ 'display_apps' ] = self.get_display_apps( trans, dataset )
else:
- rval = dataset.get_api_value()
+ rval = dataset.dictify()
except Exception, e:
rval = "Error in dataset API at listing contents: " + str( e )
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/folders.py
--- a/lib/galaxy/webapps/galaxy/api/folders.py
+++ b/lib/galaxy/webapps/galaxy/api/folders.py
@@ -35,7 +35,7 @@
# check_ownership=false since we are only displaying it.
content = self.get_library_folder( trans, id, check_ownership=False,
check_accessible=True )
- return self.encode_all_ids( trans, content.get_api_value( view='element' ) )
+ return self.encode_all_ids( trans, content.dictify( view='element' ) )
@web.expose_api
def create( self, trans, payload, **kwd ):
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/forms.py
--- a/lib/galaxy/webapps/galaxy/api/forms.py
+++ b/lib/galaxy/webapps/galaxy/api/forms.py
@@ -23,7 +23,7 @@
query = trans.sa_session.query( trans.app.model.FormDefinition )#.filter( trans.app.model.FormDefinition.table.c.deleted == False )
rval = []
for form_definition in query:
- item = form_definition.get_api_value( value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
+ item = form_definition.dictify( value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item['url'] = url_for( 'form', id=trans.security.encode_id( form_definition.id ) )
rval.append( item )
return rval
@@ -47,7 +47,7 @@
if not form_definition or not trans.user_is_admin():
trans.response.status = 400
return "Invalid form definition id ( %s ) specified." % str( form_definition_id )
- item = form_definition.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
+ item = form_definition.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item['url'] = url_for( 'form', id=form_definition_id )
return item
@@ -69,6 +69,6 @@
trans.sa_session.add( form_definition )
trans.sa_session.flush()
encoded_id = trans.security.encode_id( form_definition.id )
- item = form_definition.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
+ item = form_definition.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id } )
item['url'] = url_for( 'form', id=encoded_id )
return [ item ]
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/groups.py
--- a/lib/galaxy/webapps/galaxy/api/groups.py
+++ b/lib/galaxy/webapps/galaxy/api/groups.py
@@ -21,7 +21,7 @@
rval = []
for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted == False ):
if trans.user_is_admin():
- item = group.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+ item = group.dictify( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( group.id )
item['url'] = url_for( 'group', id=encoded_id )
rval.append( item )
@@ -65,7 +65,7 @@
"""
trans.sa_session.flush()
encoded_id = trans.security.encode_id( group.id )
- item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+ item = group.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'group', id=encoded_id )
return [ item ]
@@ -89,7 +89,7 @@
if not group:
trans.response.status = 400
return "Invalid group id ( %s ) specified." % str( group_id )
- item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+ item = group.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'group', id=group_id )
item['users_url'] = url_for( 'group_users', group_id=group_id )
item['roles_url'] = url_for( 'group_roles', group_id=group_id )
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/histories.py
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -46,14 +46,14 @@
.order_by( desc( trans.app.model.History.table.c.update_time ) )
.all() )
for history in query:
- item = history.get_api_value(value_mapper={'id':trans.security.encode_id})
+ item = history.dictify(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) )
rval.append( item )
elif trans.galaxy_session.current_history:
#No user, this must be session authentication with an anonymous user.
history = trans.galaxy_session.current_history
- item = history.get_api_value(value_mapper={'id':trans.security.encode_id})
+ item = history.dictify(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) )
rval.append(item)
@@ -139,7 +139,7 @@
trans.sa_session.add( new_history )
trans.sa_session.flush()
- item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id})
+ item = new_history.dictify(view='element', value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=item['id'] )
#TODO: copy own history
@@ -254,7 +254,7 @@
:param id: the encoded id of the history to undelete
:type payload: dict
:param payload: a dictionary containing any or all the
- fields in :func:`galaxy.model.History.get_api_value` and/or the following:
+ fields in :func:`galaxy.model.History.dictify` and/or the following:
* annotation: an annotation for the history
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -190,7 +190,7 @@
hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True )
trans.sa_session.flush()
- return hda.get_api_value()
+ return hda.dictify()
else:
# TODO: implement other "upload" methods here.
@@ -210,7 +210,7 @@
:param id: the encoded id of the history to undelete
:type payload: dict
:param payload: a dictionary containing any or all the
- fields in :func:`galaxy.model.HistoryDatasetAssociation.get_api_value`
+ fields in :func:`galaxy.model.HistoryDatasetAssociation.dictify`
and/or the following:
* annotation: an annotation for the HDA
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/item_tags.py
--- a/lib/galaxy/webapps/galaxy/api/item_tags.py
+++ b/lib/galaxy/webapps/galaxy/api/item_tags.py
@@ -49,7 +49,7 @@
return 'OK'
def _api_value( self, tag, trans, view='element' ):
- return tag.get_api_value( view=view, value_mapper={ 'id': trans.security.encode_id } )
+ return tag.dictify( view=view, value_mapper={ 'id': trans.security.encode_id } )
class HistoryContentTagsController( BaseItemTagsController ):
controller_name = "history_content_tags"
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -26,7 +26,7 @@
:rtype: list
:returns: list of dictionaries containing library information
- .. seealso:: :attr:`galaxy.model.Library.api_collection_visible_keys`
+ .. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys`
"""
log.debug( "LibrariesController.index: enter" )
query = trans.sa_session.query( trans.app.model.Library )
@@ -49,7 +49,7 @@
trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) )
rval = []
for library in query:
- item = library.get_api_value()
+ item = library.dictify()
item['url'] = url_for( route, id=trans.security.encode_id( library.id ) )
item['id'] = trans.security.encode_id( item['id'] )
rval.append( item )
@@ -71,7 +71,7 @@
:rtype: dictionary
:returns: detailed library information
- .. seealso:: :attr:`galaxy.model.Library.api_element_visible_keys`
+ .. seealso:: :attr:`galaxy.model.Library.dict_element_visible_keys`
"""
log.debug( "LibraryContentsController.show: enter" )
library_id = id
@@ -87,7 +87,7 @@
library = None
if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ) ):
raise HTTPBadRequest( detail='Invalid library id ( %s ) specified.' % id )
- item = library.get_api_value( view='element' )
+ item = library.dictify( view='element' )
#item['contents_url'] = url_for( 'contents', library_id=library_id )
item['contents_url'] = url_for( 'library_contents', library_id=library_id )
return item
@@ -145,7 +145,7 @@
:rtype: dictionary
:returns: detailed library information
- .. seealso:: :attr:`galaxy.model.Library.api_element_visible_keys`
+ .. seealso:: :attr:`galaxy.model.Library.dict_element_visible_keys`
"""
if not trans.user_is_admin():
raise HTTPForbidden( detail='You are not authorized to delete libraries.' )
@@ -162,4 +162,4 @@
library.deleted = True
trans.sa_session.add( library )
trans.sa_session.flush()
- return library.get_api_value( view='element', value_mapper={ 'id' : trans.security.encode_id } )
+ return library.dictify( view='element', value_mapper={ 'id' : trans.security.encode_id } )
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/library_contents.py
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -105,15 +105,15 @@
:rtype: dict
:returns: detailed library item information
.. seealso::
- :func:`galaxy.model.LibraryDataset.get_api_value` and
- :attr:`galaxy.model.LibraryFolder.api_element_visible_keys`
+ :func:`galaxy.model.LibraryDataset.dictify` and
+ :attr:`galaxy.model.LibraryFolder.dict_element_visible_keys`
"""
class_name, content_id = self.__decode_library_content_id( trans, id )
if class_name == 'LibraryFolder':
content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True )
else:
content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True )
- return self.encode_all_ids( trans, content.get_api_value( view='element' ) )
+ return self.encode_all_ids( trans, content.dictify( view='element' ) )
@web.expose_api
def create( self, trans, library_id, payload, **kwd ):
@@ -266,7 +266,7 @@
return { 'error' : 'user has no permission to add to library folder (%s)' %( folder_id ) }
ldda = self.copy_hda_to_library_folder( trans, hda, folder, ldda_message=ldda_message )
- ldda_dict = ldda.get_api_value()
+ ldda_dict = ldda.dictify()
rval = trans.security.encode_dict_ids( ldda_dict )
except Exception, exc:
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/permissions.py
--- a/lib/galaxy/webapps/galaxy/api/permissions.py
+++ b/lib/galaxy/webapps/galaxy/api/permissions.py
@@ -47,6 +47,6 @@
trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder )
message = "Permissions updated for library '%s'." % library.name
- item = library.get_api_value( view='element' )
+ item = library.dictify( view='element' )
return item
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/quotas.py
--- a/lib/galaxy/webapps/galaxy/api/quotas.py
+++ b/lib/galaxy/webapps/galaxy/api/quotas.py
@@ -34,7 +34,7 @@
route = 'quota'
query = query.filter( trans.app.model.Quota.table.c.deleted == False )
for quota in query:
- item = quota.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+ item = quota.dictify( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( quota.id )
item['url'] = url_for( route, id=encoded_id )
rval.append( item )
@@ -49,7 +49,7 @@
Displays information about a quota.
"""
quota = self.get_quota( trans, id, deleted=util.string_as_bool( deleted ) )
- return quota.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+ return quota.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
@web.expose_api
@web.require_admin
@@ -67,7 +67,7 @@
quota, message = self._create_quota( params )
except ActionInputError, e:
raise HTTPBadRequest( detail=str( e ) )
- item = quota.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+ item = quota.dictify( value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'quota', id=trans.security.encode_id( quota.id ) )
item['message'] = message
return item
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/request_types.py
--- a/lib/galaxy/webapps/galaxy/api/request_types.py
+++ b/lib/galaxy/webapps/galaxy/api/request_types.py
@@ -19,7 +19,7 @@
"""
rval = []
for request_type in trans.app.security_agent.get_accessible_request_types( trans, trans.user ):
- item = request_type.get_api_value( value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
+ item = request_type.dictify( value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( request_type.id )
item['url'] = url_for( 'request_type', id=encoded_id )
rval.append( item )
@@ -47,7 +47,7 @@
if not trans.app.security_agent.can_access_request_type( trans.user.all_roles(), request_type ):
trans.response.status = 400
return "No permission to access request_type ( %s )." % str( request_type_id )
- item = request_type.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
+ item = request_type.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
item['url'] = url_for( 'request_type', id=request_type_id )
return item
@@ -97,6 +97,6 @@
trans.sa_session.add( request_type )
trans.sa_session.flush()
encoded_id = trans.security.encode_id( request_type.id )
- item = request_type.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
+ item = request_type.dictify( view='element', value_mapper={ 'id': trans.security.encode_id, 'request_form_id': trans.security.encode_id, 'sample_form_id': trans.security.encode_id } )
item['url'] = url_for( 'request_type', id=encoded_id )
return [ item ]
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/requests.py
--- a/lib/galaxy/webapps/galaxy/api/requests.py
+++ b/lib/galaxy/webapps/galaxy/api/requests.py
@@ -30,7 +30,7 @@
.all()
rval = []
for request in query:
- item = request.get_api_value()
+ item = request.dictify()
item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) )
item['id'] = trans.security.encode_id( item['id'] )
if trans.user_is_admin():
@@ -55,7 +55,7 @@
if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ):
trans.response.status = 400
return "Invalid request id ( %s ) specified." % str( request_id )
- item = request.get_api_value()
+ item = request.dictify()
item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) )
item['id'] = trans.security.encode_id( item['id'] )
item['user'] = request.user.email
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/roles.py
--- a/lib/galaxy/webapps/galaxy/api/roles.py
+++ b/lib/galaxy/webapps/galaxy/api/roles.py
@@ -18,7 +18,7 @@
rval = []
for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted == False ):
if trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role ):
- item = role.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+ item = role.dictify( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( role.id )
item['url'] = url_for( 'role', id=encoded_id )
rval.append( item )
@@ -43,7 +43,7 @@
if not role or not (trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role )):
trans.response.status = 400
return "Invalid role id ( %s ) specified." % str( role_id )
- item = role.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+ item = role.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'role', id=role_id )
return item
@@ -81,6 +81,6 @@
trans.app.security_agent.associate_group_role( group, role )
trans.sa_session.flush()
encoded_id = trans.security.encode_id( role.id )
- item = role.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } )
+ item = role.dictify( view='element', value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( 'role', id=encoded_id )
return [ item ]
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/samples.py
--- a/lib/galaxy/webapps/galaxy/api/samples.py
+++ b/lib/galaxy/webapps/galaxy/api/samples.py
@@ -35,7 +35,7 @@
return "Invalid request id ( %s ) specified." % str( request_id )
rval = []
for sample in request.samples:
- item = sample.get_api_value()
+ item = sample.dictify()
item['url'] = url_for( 'samples',
request_id=trans.security.encode_id( request_id ),
id=trans.security.encode_id( sample.id ) )
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -45,7 +45,7 @@
.order_by( trans.app.model.ToolShedRepository.table.c.name ) \
.all()
for tool_shed_repository in query:
- tool_shed_repository_dict = tool_shed_repository.get_api_value( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) )
+ tool_shed_repository_dict = tool_shed_repository.dictify( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) )
tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( tool_shed_repository.id ) )
@@ -402,7 +402,7 @@
repair_dict = repository_util.repair_tool_shed_repository( trans,
repository,
encoding_util.tool_shed_encode( repo_info_dict ) )
- repository_dict = repository.get_api_value( value_mapper=default_tool_shed_repository_value_mapper( trans, repository ) )
+ repository_dict = repository.dictify( value_mapper=default_tool_shed_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/tools.py
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -106,7 +106,7 @@
outputs = rval[ "outputs" ]
#TODO:?? poss. only return ids?
for output in output_datasets:
- output_dict = output.get_api_value()
+ output_dict = output.dictify()
outputs.append( trans.security.encode_dict_ids( output_dict ) )
return rval
@@ -412,7 +412,7 @@
if joda.name == output_name:
output_dataset = joda.dataset
- dataset_dict = output_dataset.get_api_value()
+ dataset_dict = output_dataset.dictify()
dataset_dict[ 'id' ] = trans.security.encode_id( dataset_dict[ 'id' ] )
dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset );
return dataset_dict
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/users.py
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -33,13 +33,13 @@
query = query.filter( trans.app.model.User.table.c.deleted == False )
# special case: user can see only their own user
if not trans.user_is_admin():
- item = trans.user.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+ item = trans.user.dictify( value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( route, id=item['id'] )
item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
return [item]
for user in query:
- item = user.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
+ item = user.dictify( value_mapper={ 'id': trans.security.encode_id } )
#TODO: move into api_values
item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
item['url'] = url_for( route, id=item['id'] )
@@ -77,7 +77,7 @@
raise
else:
raise HTTPBadRequest( detail='Invalid user id ( %s ) specified' % id )
- item = user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id,
+ item = user.dictify( view='element', value_mapper={ 'id': trans.security.encode_id,
'total_disk_usage': float } )
#TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??)
#TODO: works with other users (from admin)??
@@ -94,7 +94,7 @@
raise HTTPNotImplemented( detail='User creation is not allowed in this Galaxy instance' )
if trans.app.config.use_remote_user and trans.user_is_admin():
user = trans.get_or_create_remote_user(remote_user_email=payload['remote_user_email'])
- item = user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id,
+ item = user.dictify( view='element', value_mapper={ 'id': trans.security.encode_id,
'total_disk_usage': float } )
else:
raise HTTPNotImplemented()
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/visualizations.py
--- a/lib/galaxy/webapps/galaxy/api/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/api/visualizations.py
@@ -212,7 +212,7 @@
# this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs
valid_but_uneditable_keys = (
'id', 'model_class'
- #TODO: fill out when we create get_api_value, get_dict, whatevs
+ #TODO: fill out when we create dictify, get_dict, whatevs
)
#TODO: deleted
#TODO: importable
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -31,7 +31,7 @@
for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).filter_by(
user=trans.user, deleted=False).order_by(
desc(trans.app.model.StoredWorkflow.table.c.update_time)).all():
- item = wf.get_api_value(value_mapper={'id':trans.security.encode_id})
+ item = wf.dictify(value_mapper={'id':trans.security.encode_id})
encoded_id = trans.security.encode_id(wf.id)
item['url'] = url_for('workflow', id=encoded_id)
rval.append(item)
@@ -39,7 +39,7 @@
user=trans.user ).join( 'stored_workflow' ).filter(
trans.app.model.StoredWorkflow.deleted == False ).order_by(
desc( trans.app.model.StoredWorkflow.update_time ) ).all():
- item = wf_sa.stored_workflow.get_api_value(value_mapper={'id':trans.security.encode_id})
+ item = wf_sa.stored_workflow.dictify(value_mapper={'id':trans.security.encode_id})
encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
item['url'] = url_for('workflow', id=encoded_id)
rval.append(item)
@@ -67,7 +67,7 @@
except:
trans.response.status = 400
return "That workflow does not exist."
- item = stored_workflow.get_api_value(view='element', value_mapper={'id':trans.security.encode_id})
+ item = stored_workflow.dictify(view='element', value_mapper={'id':trans.security.encode_id})
item['url'] = url_for('workflow', id=workflow_id)
latest_workflow = stored_workflow.latest_workflow
inputs = {}
@@ -329,7 +329,7 @@
# return list
rval= [];
- item = workflow.get_api_value(value_mapper={'id':trans.security.encode_id})
+ item = workflow.dictify(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for('workflow', id=encoded_id)
rval.append(item);
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/galaxy/controllers/visualization.py
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -875,7 +875,7 @@
# Add tool, dataset attributes to config based on id.
tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] )
viz_config[ 'tool' ] = tool.to_dict( trans, for_display=True )
- viz_config[ 'dataset' ] = dataset.get_api_value()
+ viz_config[ 'dataset' ] = dataset.dictify()
return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config )
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -113,7 +113,7 @@
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
encoded_repository_id = trans.security.encode_id( repository.id )
- repository_dict = repository.get_api_value( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
+ repository_dict = repository.dictify( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=encoded_repository_id )
@@ -129,7 +129,7 @@
changeset_revision = new_changeset_revision
if repository_metadata:
encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id )
- repository_metadata_dict = repository_metadata.get_api_value( view='collection',
+ repository_metadata_dict = repository_metadata.dictify( view='collection',
value_mapper=default_repository_metadata_value_mapper( trans, repository_metadata ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
@@ -164,7 +164,7 @@
.order_by( trans.app.model.Repository.table.c.name ) \
.all()
for repository in query:
- repository_dict = repository.get_api_value( view='collection', value_mapper=default_repository_value_mapper( trans, repository ) )
+ repository_dict = repository.dictify( view='collection', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
@@ -187,7 +187,7 @@
# Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
try:
repository = suc.get_repository_in_tool_shed( trans, id )
- repository_dict = repository.get_api_value( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
+ repository_dict = repository.dictify( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/tool_shed/api/repository_revisions.py
--- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
+++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
@@ -127,7 +127,7 @@
.order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \
.all()
for repository_metadata in query:
- repository_metadata_dict = repository_metadata.get_api_value( view='collection',
+ repository_metadata_dict = repository_metadata.dictify( view='collection',
value_mapper=default_value_mapper( trans, repository_metadata ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 lib/galaxy/webapps/tool_shed/model/__init__.py
--- a/lib/galaxy/webapps/tool_shed/model/__init__.py
+++ b/lib/galaxy/webapps/tool_shed/model/__init__.py
@@ -4,7 +4,7 @@
from galaxy import util
from galaxy.util.bunch import Bunch
from galaxy.util.hash_util import new_secure_hash
-from galaxy.model.item_attrs import APIItem
+from galaxy.model.item_attrs import DictifiableMixin
import tool_shed.repository_types.util as rt_util
from galaxy import eggs
@@ -19,9 +19,9 @@
pass
-class User( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'email' )
- api_element_visible_keys = ( 'id', 'email', 'username' )
+class User( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'email' )
+ dict_element_visible_keys = ( 'id', 'email', 'username' )
def __init__( self, email=None, password=None ):
self.email = email
@@ -61,18 +61,18 @@
return 0
-class Group( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name' )
- api_element_visible_keys = ( 'id', 'name' )
+class Group( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name' )
+ dict_element_visible_keys = ( 'id', 'name' )
def __init__( self, name = None ):
self.name = name
self.deleted = False
-class Role( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name' )
- api_element_visible_keys = ( 'id', 'name', 'description', 'type' )
+class Role( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name' )
+ dict_element_visible_keys = ( 'id', 'name', 'description', 'type' )
private_id = None
types = Bunch(
PRIVATE = 'private',
@@ -130,9 +130,9 @@
self.prev_session_id = prev_session_id
-class Repository( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' )
- api_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded',
+class Repository( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' )
+ dict_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded',
'deprecated' )
file_states = Bunch( NORMAL = 'n',
NEEDS_MERGING = 'm',
@@ -155,7 +155,7 @@
self.deprecated = deprecated
def as_dict( self, value_mapper=None ):
- return self.get_api_value( view='element', value_mapper=value_mapper )
+ return self.dictify( view='element', value_mapper=value_mapper )
def can_change_type( self, app ):
# Allow changing the type only if the repository has no contents, has never been installed, or has never been changed from
@@ -175,7 +175,7 @@
return True
return False
- def get_api_value( self, view='collection', value_mapper=None ):
+ def dictify( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -244,10 +244,10 @@
fp.close()
-class RepositoryMetadata( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'has_repository_dependencies', 'includes_datatypes',
+class RepositoryMetadata( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'has_repository_dependencies', 'includes_datatypes',
'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows' )
- api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', 'do_not_test',
+ dict_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', 'do_not_test',
'test_install_error', 'time_last_tested', 'tool_test_results', 'has_repository_dependencies', 'includes_datatypes',
'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows' )
@@ -284,9 +284,9 @@
return False
def as_dict( self, value_mapper=None ):
- return self.get_api_value( view='element', value_mapper=value_mapper )
+ return self.dictify( view='element', value_mapper=value_mapper )
- def get_api_value( self, view='collection', value_mapper=None ):
+ def dictify( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -304,9 +304,9 @@
return rval
-class SkipToolTest( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'repository_metadata_id', 'initial_changeset_revision' )
- api_element_visible_keys = ( 'id', 'repository_metadata_id', 'initial_changeset_revision', 'comment' )
+class SkipToolTest( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'repository_metadata_id', 'initial_changeset_revision' )
+ dict_element_visible_keys = ( 'id', 'repository_metadata_id', 'initial_changeset_revision', 'comment' )
def __init__( self, id=None, repository_metadata_id=None, initial_changeset_revision=None, comment=None ):
self.id = id
@@ -315,9 +315,9 @@
self.comment = comment
def as_dict( self, value_mapper=None ):
- return self.get_api_value( view='element', value_mapper=value_mapper )
+ return self.dictify( view='element', value_mapper=value_mapper )
- def get_api_value( self, view='collection', value_mapper=None ):
+ def dictify( self, view='collection', value_mapper=None ):
if value_mapper is None:
value_mapper = {}
rval = {}
@@ -335,9 +335,9 @@
return rval
-class RepositoryReview( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' )
- api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' )
+class RepositoryReview( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' )
+ dict_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' )
approved_states = Bunch( NO='no', YES='yes' )
def __init__( self, repository_id=None, changeset_revision=None, user_id=None, rating=None, deleted=False ):
@@ -347,9 +347,9 @@
self.rating = rating
self.deleted = deleted
-class ComponentReview( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' )
- api_element_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' )
+class ComponentReview( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' )
+ dict_element_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' )
approved_states = Bunch( NO='no', YES='yes', NA='not_applicable' )
def __init__( self, repository_review_id=None, component_id=None, comment=None, private=False, approved=False, rating=None, deleted=False ):
@@ -389,9 +389,9 @@
self.repository = repository
-class Category( object, APIItem ):
- api_collection_visible_keys = ( 'id', 'name', 'description', 'deleted' )
- api_element_visible_keys = ( 'id', 'name', 'description', 'deleted' )
+class Category( object, DictifiableMixin ):
+ dict_collection_visible_keys = ( 'id', 'name', 'description', 'deleted' )
+ dict_element_visible_keys = ( 'id', 'name', 'description', 'deleted' )
def __init__( self, name=None, description=None, deleted=False ):
self.name = name
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 templates/webapps/galaxy/base_panels.mako
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -16,7 +16,7 @@
"""Bootstrapping user API JSON"""
#TODO: move into common location (poss. BaseController)
if trans.user:
- user_dict = trans.user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id,
+ user_dict = trans.user.dictify( view='element', value_mapper={ 'id': trans.security.encode_id,
'total_disk_usage': float } )
user_dict['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
else:
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 templates/webapps/galaxy/dataset/display.mako
--- a/templates/webapps/galaxy/dataset/display.mako
+++ b/templates/webapps/galaxy/dataset/display.mako
@@ -20,7 +20,7 @@
require(['mvc/data'], function(data) {
data.createTabularDatasetChunkedView(
// Dataset config. TODO: encode id.
- _.extend( ${h.to_json_string( item.get_api_value() )},
+ _.extend( ${h.to_json_string( item.dictify() )},
{
chunk_url: "${h.url_for( controller='/dataset', action='display',
dataset_id=trans.security.encode_id( item.id ))}",
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 templates/webapps/galaxy/dataset/tabular_chunked.mako
--- a/templates/webapps/galaxy/dataset/tabular_chunked.mako
+++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako
@@ -19,7 +19,7 @@
require(['mvc/data'], function(data) {
data.createTabularDatasetChunkedView(
- _.extend( ${h.to_json_string( trans.security.encode_dict_ids( dataset.get_api_value() ) )},
+ _.extend( ${h.to_json_string( trans.security.encode_dict_ids( dataset.dictify() ) )},
{
url_viz: "${h.url_for( controller='/visualization')}",
chunk_url: "${h.url_for( controller='/dataset', action='display',
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 templates/webapps/galaxy/galaxy.masthead.mako
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -4,7 +4,7 @@
"""Bootstrapping user API JSON"""
#TODO: move into common location (poss. BaseController)
if trans.user:
- user_dict = trans.user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id,
+ user_dict = trans.user.dictify( view='element', value_mapper={ 'id': trans.security.encode_id,
'total_disk_usage': float } )
user_dict['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
else:
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 templates/webapps/galaxy/visualization/scatterplot.mako
--- a/templates/webapps/galaxy/visualization/scatterplot.mako
+++ b/templates/webapps/galaxy/visualization/scatterplot.mako
@@ -222,7 +222,7 @@
<script type="text/javascript">
$(function(){
- var hda = ${h.to_json_string( trans.security.encode_dict_ids( hda.get_api_value() ) )},
+ var hda = ${h.to_json_string( trans.security.encode_dict_ids( hda.dictify() ) )},
querySettings = ${h.to_json_string( query_args )},
chartConfig = _.extend( querySettings, {
containerSelector : '#chart',
diff -r a699decd482ce7732ea61ffb8e13714a0f991381 -r 4f4e01316260d300dc10da137cbbd5905114b7f5 templates/webapps/galaxy/visualization/v_fwork_test.mako
--- a/templates/webapps/galaxy/visualization/v_fwork_test.mako
+++ b/templates/webapps/galaxy/visualization/v_fwork_test.mako
@@ -19,7 +19,7 @@
<%def name="process_hda( hda )"><%
- hda_dict = hda.get_api_value()
+ hda_dict = hda.dictify()
hda_dict[ 'id' ] = trans.security.encode_id( hda_dict[ 'id' ] )
hda_dict[ 'history_id' ] = trans.security.encode_id( hda_dict[ 'history_id' ] )
del hda_dict[ 'peek' ]
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