commit/galaxy-central: dannon: Fix (kind of a guess as to the intended functionality) input_dbkey error.
by commits-noreply＠bitbucket.org 19 May '14
by commits-noreply＠bitbucket.org 19 May '14
19 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d62fd7469c62/
Changeset: d62fd7469c62
Branch: next-stable
User: dannon
Date: 2014-05-19 23:42:05
Summary: Fix (kind of a guess as to the intended functionality) input_dbkey error.
Affected #: 1 file
diff -r e7bcba2bec53e16c8e11bb136da9f8aad9e430ba -r d62fd7469c626064d8fe9792ea4584c57b5ed431 lib/galaxy/util/dbkeys.py
--- a/lib/galaxy/util/dbkeys.py
+++ b/lib/galaxy/util/dbkeys.py
@@ -55,9 +55,9 @@
chrom_info = db_dataset.file_name
else:
# -- Get chrom_info (len file) from either a custom or built-in build. --
- if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
+ if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
# Custom build.
- custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
+ custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ]
# HACK: the attempt to get chrom_info below will trigger the
# fasta-to-len converter if the dataset is not available or,
# which will in turn create a recursive loop when
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e7bcba2bec53/
Changeset: e7bcba2bec53
Branch: next-stable
User: jmchilton
Date: 2014-05-19 23:18:02
Summary: HACK: Fix circular dependency non-sense related to tools and dataset collections.
https://gist.github.com/jmchilton/6e19d248002b1080e8ba.
Affected #: 1 file
diff -r c822084e6e5407c6ac80f999fa313808049e58f7 -r e7bcba2bec53e16c8e11bb136da9f8aad9e430ba lib/galaxy/tools/parameters/meta.py
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -2,8 +2,6 @@
from galaxy import model
from galaxy import util
from galaxy import exceptions
-from galaxy.dataset_collections import matching
-from galaxy.dataset_collections import subcollections
import logging
log = logging.getLogger( __name__ )
@@ -29,6 +27,7 @@
else:
return permutations.input_classification.SINGLE, incoming[ input_key ]
+ from galaxy.dataset_collections import matching
collections_to_match = matching.CollectionsToMatch()
def collection_classifier( input_key ):
@@ -52,6 +51,7 @@
hdc = trans.sa_session.query( model.HistoryDatasetCollectionAssociation ).get( hdc_id )
collections_to_match.add( input_key, hdc, subcollection_type=subcollection_type )
if subcollection_type is not None:
+ from galaxy.dataset_collections import subcollections
subcollection_elements = subcollections.split_dataset_collection_instance( hdc, subcollection_type )
return permutations.input_classification.MATCHED, subcollection_elements
else:
https://bitbucket.org/galaxy/galaxy-central/commits/05302ebc7377/
Changeset: 05302ebc7377
User: jmchilton
Date: 2014-05-19 23:18:31
Summary: Merge next-stable.
Affected #: 1 file
diff -r 35afd36f9014915c4c82f65b1c52a6636f48328e -r 05302ebc73772d383ef55781e7c59d7365258e5b lib/galaxy/tools/parameters/meta.py
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -2,8 +2,6 @@
from galaxy import model
from galaxy import util
from galaxy import exceptions
-from galaxy.dataset_collections import matching
-from galaxy.dataset_collections import subcollections
import logging
log = logging.getLogger( __name__ )
@@ -29,6 +27,7 @@
else:
return permutations.input_classification.SINGLE, incoming[ input_key ]
+ from galaxy.dataset_collections import matching
collections_to_match = matching.CollectionsToMatch()
def collection_classifier( input_key ):
@@ -52,6 +51,7 @@
hdc = trans.sa_session.query( model.HistoryDatasetCollectionAssociation ).get( hdc_id )
collections_to_match.add( input_key, hdc, subcollection_type=subcollection_type )
if subcollection_type is not None:
+ from galaxy.dataset_collections import subcollections
subcollection_elements = subcollections.split_dataset_collection_instance( hdc, subcollection_type )
return permutations.input_classification.MATCHED, subcollection_elements
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
19 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/35afd36f9014/
Changeset: 35afd36f9014
User: dannon
Date: 2014-05-19 22:56:28
Summary: Merge from next-stable.
Affected #: 7 files
diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -18,6 +18,7 @@
from galaxy.tools.data_manager.manager import DataManagers
from galaxy.jobs import metrics as job_metrics
from galaxy.web.base import pluginframework
+from galaxy.queue_worker import GalaxyQueueWorker
import logging
log = logging.getLogger( __name__ )
@@ -146,6 +147,10 @@
# Initialize the external service types
self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self )
self.model.engine.dispose()
+ self.control_worker = GalaxyQueueWorker(self,
+ galaxy.queues.control_queue_from_config(self.config),
+ galaxy.queue_worker.control_message_to_task)
+ self.control_worker.start()
def shutdown( self ):
self.job_manager.shutdown()
diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -340,6 +340,17 @@
amqp_config = {}
for k, v in amqp_config:
self.amqp[k] = v
+ # Galaxy internal control queue configuration.
+ # If specified in universe, use it, otherwise we use whatever 'real'
+ # database is specified. Lastly, we create and use new sqlite database
+ # (to minimize locking) as a final option.
+ if 'amqp_internal_connection' in kwargs:
+ self.amqp_internal_connection = kwargs.get('amqp_internal_connection')
+ # TODO Get extra amqp args as necessary for ssl
+ elif 'database_connection' in kwargs:
+ self.amqp_internal_connection = "sqlalchemy+"+self.database_connection
+ else:
+ self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path( "database/control.sqlite", self.root )
self.biostar_url = kwargs.get( 'biostar_url', None )
self.biostar_key_name = kwargs.get( 'biostar_key_name', None )
self.biostar_key = kwargs.get( 'biostar_key', None )
diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/queue_worker.py
--- /dev/null
+++ b/lib/galaxy/queue_worker.py
@@ -0,0 +1,94 @@
+"""
+Galaxy control queue and worker. This is used to handle 'app' control like
+reloading the toolbox, etc., across multiple processes.
+"""
+
+import logging
+import threading
+import galaxy.queues
+from galaxy import eggs, util
+eggs.require('kombu')
+
+from kombu import Connection
+from kombu.mixins import ConsumerMixin
+from kombu.pools import producers
+
+
+log = logging.getLogger(__name__)
+
+
+class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
+ """
+ This is a flexible worker for galaxy's queues. Each process, web or
+ handler, will have one of these used for dispatching so called 'control'
+ tasks.
+ """
+ def __init__(self, app, queue, task_mapping):
+ super(GalaxyQueueWorker, self).__init__()
+ log.info("Initalizing Galaxy Queue Worker on %s" % app.config.amqp_internal_connection)
+ self.connection = Connection(app.config.amqp_internal_connection)
+ self.app = app
+ # Eventually we may want different workers w/ their own queues and task
+ # mappings. Right now, there's only the one.
+ self.control_queue = queue
+ self.task_mapping = task_mapping
+ self.declare_queues = galaxy.queues.all_control_queues_for_declare(app.config)
+ # TODO we may want to purge the queue at the start to avoid executing
+ # stale 'reload_tool', etc messages. This can happen if, say, a web
+ # process goes down and messages get sent before it comes back up.
+ # Those messages will no longer be useful (in any current case)
+
+ def get_consumers(self, Consumer, channel):
+ return [Consumer(queues=self.control_queue,
+ callbacks=[self.process_task])]
+
+ def process_task(self, body, message):
+ if body['task'] in self.task_mapping:
+ if body.get('noop', None) != self.app.config.server_name:
+ try:
+ f = self.task_mapping[body['task']]
+ log.debug("Instance recieved '%s' task, executing now." % body['task'])
+ f(self.app, **body['kwargs'])
+ except Exception:
+ # this shouldn't ever throw an exception, but...
+ log.exception("Error running control task type: %s" % body['task'])
+ else:
+ log.warning("Recieved a malformed task message:\n%s" % body)
+ message.ack()
+
+
+def send_control_task(trans, task, noop_self=False, kwargs={}):
+ log.info("Sending %s control task." % task)
+ payload = {'task': task,
+ 'kwargs': kwargs}
+ if noop_self:
+ payload['noop'] = trans.app.config.server_name
+ c = Connection(trans.app.config.amqp_internal_connection)
+ with producers[c].acquire(block=True) as producer:
+ producer.publish(payload, exchange=galaxy.queues.galaxy_exchange,
+ declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config),
+ routing_key='control')
+
+
+# Tasks -- to be reorganized into a separate module as appropriate. This is
+# just an example method. Ideally this gets pushed into atomic tasks, whether
+# where they're currently invoked, or elsewhere. (potentially using a dispatch
+# decorator).
+def reload_tool(app, **kwargs):
+ params = util.Params(kwargs)
+ tool_id = params.get('tool_id', None)
+ log.debug("Executing reload tool task for %s" % tool_id)
+ if tool_id:
+ app.toolbox.reload_tool_by_id( tool_id )
+ else:
+ log.error("Reload tool invoked without tool id.")
+
+
+def reload_tool_data_tables(app, **kwargs):
+ params = util.Params(kwargs)
+ log.debug("Executing tool data table reload for %s" % params.get('table_names', 'all tables'))
+ table_names = app.tool_data_tables.reload_tables( table_names=params.get('table_name', None))
+ log.debug("Finished data table reload for %s" % table_names)
+
+control_message_to_task = { 'reload_tool': reload_tool,
+ 'reload_tool_data_tables': reload_tool_data_tables}
diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/queues.py
--- /dev/null
+++ b/lib/galaxy/queues.py
@@ -0,0 +1,32 @@
+"""
+
+All message queues used by Galaxy
+
+"""
+
+from galaxy import eggs
+
+eggs.require("kombu")
+from kombu import Exchange, Queue
+
+ALL_CONTROL = "control.*"
+galaxy_exchange = Exchange('galaxy_core_exchange', type='topic')
+
+
+def all_control_queues_for_declare(config):
+ """
+ For in-memory routing (used by sqlalchemy-based transports), we need to be able to
+ build the entire routing table in producers.
+
+ Refactor later to actually persist this somewhere instead of building it repeatedly.
+ """
+ return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for q in config.server_names]
+
+
+def control_queue_from_config(config):
+ """
+ Returns a Queue instance with the correct name and routing key for this
+ galaxy process's config
+ """
+ return Queue("control.%s" % config.server_name, galaxy_exchange,
+ routing_key='control')
diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/web/base/controllers/admin.py
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -5,6 +5,7 @@
from galaxy.util import inflector
from galaxy.web.form_builder import CheckboxField
from string import punctuation as PUNCTUATION
+import galaxy.queue_worker
log = logging.getLogger( __name__ )
@@ -62,8 +63,9 @@
toolbox = self.app.toolbox
tool_id = None
if params.get( 'reload_tool_button', False ):
- tool_id = params.tool_id
- message, status = toolbox.reload_tool_by_id( tool_id )
+ tool_id = params.get('tool_id', None)
+ galaxy.queue_worker.send_control_task(trans, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id} )
+ message, status = trans.app.toolbox.reload_tool_by_id( tool_id)
return trans.fill_template( '/admin/reload_tool.mako',
tool_id=tool_id,
toolbox=toolbox,
diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e lib/galaxy/webapps/galaxy/controllers/data_manager.py
--- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py
+++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
@@ -1,6 +1,7 @@
+import galaxy.queue_worker
from galaxy import web
+from galaxy.util.json import from_json_string
from galaxy.web.base.controller import BaseUIController
-from galaxy.util.json import from_json_string
import pkg_resources;
pkg_resources.require( "Paste" )
@@ -90,6 +91,9 @@
table_name = table_name.split( "," )
# Reload the tool data tables
table_names = self.app.tool_data_tables.reload_tables( table_names=table_name )
+ galaxy.queue_worker.send_control_task(trans, 'reload_tool_data_tables',
+ noop_self=True,
+ kwargs={'table_name': table_name} )
redirect_url = None
if table_names:
status = 'done'
diff -r 174b6a2281e53793a8188ba2b2792d0dd220d362 -r 35afd36f9014915c4c82f65b1c52a6636f48328e universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -821,7 +821,21 @@
#user_tool_section_filters = examples:restrict_text
#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode
-# ---- Galaxy Message Queue -------------------------------------------------
+# Galaxy Application Internal Message Queue
+
+# Galaxy uses AMQP internally TODO more documentation on what for.
+# For examples, see http://ask.github.io/kombu/userguide/connections.html
+#
+# Without specifying anything here, galaxy will first attempt to use your
+# specified database_connection above. If that's not specified either, Galaxy
+# will automatically create and use a separate sqlite database located in your
+# <galaxy>/database folder (indicated in the commented out line below).
+
+#amqp_internal_connection = "sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE"
+
+
+
+# ---- Galaxy External Message Queue -------------------------------------------------
# Galaxy uses AMQ protocol to receive messages from external sources like
# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
commit/galaxy-central: dannon: Initial internal control message queue for IPC implementation. Needs significant refactoring, as noted in some TODOs, but this is a minimally functional version so it makes the next-stable cutoff. Currently only handles reloading tools and data tables, but adding additional tasks is simple and should be straightforward.
by commits-noreply＠bitbucket.org 19 May '14
by commits-noreply＠bitbucket.org 19 May '14
19 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c822084e6e54/
Changeset: c822084e6e54
Branch: next-stable
User: dannon
Date: 2014-05-19 22:56:08
Summary: Initial internal control message queue for IPC implementation. Needs significant refactoring, as noted in some TODOs, but this is a minimally functional version so it makes the next-stable cutoff. Currently only handles reloading tools and data tables, but adding additional tasks is simple and should be straightforward.
Affected #: 7 files
diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -18,6 +18,7 @@
from galaxy.tools.data_manager.manager import DataManagers
from galaxy.jobs import metrics as job_metrics
from galaxy.web.base import pluginframework
+from galaxy.queue_worker import GalaxyQueueWorker
import logging
log = logging.getLogger( __name__ )
@@ -146,6 +147,10 @@
# Initialize the external service types
self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self )
self.model.engine.dispose()
+ self.control_worker = GalaxyQueueWorker(self,
+ galaxy.queues.control_queue_from_config(self.config),
+ galaxy.queue_worker.control_message_to_task)
+ self.control_worker.start()
def shutdown( self ):
self.job_manager.shutdown()
diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -340,6 +340,17 @@
amqp_config = {}
for k, v in amqp_config:
self.amqp[k] = v
+ # Galaxy internal control queue configuration.
+ # If specified in universe, use it, otherwise we use whatever 'real'
+ # database is specified. Lastly, we create and use new sqlite database
+ # (to minimize locking) as a final option.
+ if 'amqp_internal_connection' in kwargs:
+ self.amqp_internal_connection = kwargs.get('amqp_internal_connection')
+ # TODO Get extra amqp args as necessary for ssl
+ elif 'database_connection' in kwargs:
+ self.amqp_internal_connection = "sqlalchemy+"+self.database_connection
+ else:
+ self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path( "database/control.sqlite", self.root )
self.biostar_url = kwargs.get( 'biostar_url', None )
self.biostar_key_name = kwargs.get( 'biostar_key_name', None )
self.biostar_key = kwargs.get( 'biostar_key', None )
diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/queue_worker.py
--- /dev/null
+++ b/lib/galaxy/queue_worker.py
@@ -0,0 +1,94 @@
+"""
+Galaxy control queue and worker. This is used to handle 'app' control like
+reloading the toolbox, etc., across multiple processes.
+"""
+
+import logging
+import threading
+import galaxy.queues
+from galaxy import eggs, util
+eggs.require('kombu')
+
+from kombu import Connection
+from kombu.mixins import ConsumerMixin
+from kombu.pools import producers
+
+
+log = logging.getLogger(__name__)
+
+
+class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
+ """
+ This is a flexible worker for galaxy's queues. Each process, web or
+ handler, will have one of these used for dispatching so called 'control'
+ tasks.
+ """
+ def __init__(self, app, queue, task_mapping):
+ super(GalaxyQueueWorker, self).__init__()
+ log.info("Initalizing Galaxy Queue Worker on %s" % app.config.amqp_internal_connection)
+ self.connection = Connection(app.config.amqp_internal_connection)
+ self.app = app
+ # Eventually we may want different workers w/ their own queues and task
+ # mappings. Right now, there's only the one.
+ self.control_queue = queue
+ self.task_mapping = task_mapping
+ self.declare_queues = galaxy.queues.all_control_queues_for_declare(app.config)
+ # TODO we may want to purge the queue at the start to avoid executing
+ # stale 'reload_tool', etc messages. This can happen if, say, a web
+ # process goes down and messages get sent before it comes back up.
+ # Those messages will no longer be useful (in any current case)
+
+ def get_consumers(self, Consumer, channel):
+ return [Consumer(queues=self.control_queue,
+ callbacks=[self.process_task])]
+
+ def process_task(self, body, message):
+ if body['task'] in self.task_mapping:
+ if body.get('noop', None) != self.app.config.server_name:
+ try:
+ f = self.task_mapping[body['task']]
+ log.debug("Instance recieved '%s' task, executing now." % body['task'])
+ f(self.app, **body['kwargs'])
+ except Exception:
+ # this shouldn't ever throw an exception, but...
+ log.exception("Error running control task type: %s" % body['task'])
+ else:
+ log.warning("Recieved a malformed task message:\n%s" % body)
+ message.ack()
+
+
+def send_control_task(trans, task, noop_self=False, kwargs={}):
+ log.info("Sending %s control task." % task)
+ payload = {'task': task,
+ 'kwargs': kwargs}
+ if noop_self:
+ payload['noop'] = trans.app.config.server_name
+ c = Connection(trans.app.config.amqp_internal_connection)
+ with producers[c].acquire(block=True) as producer:
+ producer.publish(payload, exchange=galaxy.queues.galaxy_exchange,
+ declare=[galaxy.queues.galaxy_exchange] + galaxy.queues.all_control_queues_for_declare(trans.app.config),
+ routing_key='control')
+
+
+# Tasks -- to be reorganized into a separate module as appropriate. This is
+# just an example method. Ideally this gets pushed into atomic tasks, whether
+# where they're currently invoked, or elsewhere. (potentially using a dispatch
+# decorator).
+def reload_tool(app, **kwargs):
+ params = util.Params(kwargs)
+ tool_id = params.get('tool_id', None)
+ log.debug("Executing reload tool task for %s" % tool_id)
+ if tool_id:
+ app.toolbox.reload_tool_by_id( tool_id )
+ else:
+ log.error("Reload tool invoked without tool id.")
+
+
+def reload_tool_data_tables(app, **kwargs):
+ params = util.Params(kwargs)
+ log.debug("Executing tool data table reload for %s" % params.get('table_names', 'all tables'))
+ table_names = app.tool_data_tables.reload_tables( table_names=params.get('table_name', None))
+ log.debug("Finished data table reload for %s" % table_names)
+
+control_message_to_task = { 'reload_tool': reload_tool,
+ 'reload_tool_data_tables': reload_tool_data_tables}
diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/queues.py
--- /dev/null
+++ b/lib/galaxy/queues.py
@@ -0,0 +1,32 @@
+"""
+
+All message queues used by Galaxy
+
+"""
+
+from galaxy import eggs
+
+eggs.require("kombu")
+from kombu import Exchange, Queue
+
+ALL_CONTROL = "control.*"
+galaxy_exchange = Exchange('galaxy_core_exchange', type='topic')
+
+
+def all_control_queues_for_declare(config):
+ """
+ For in-memory routing (used by sqlalchemy-based transports), we need to be able to
+ build the entire routing table in producers.
+
+ Refactor later to actually persist this somewhere instead of building it repeatedly.
+ """
+ return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for q in config.server_names]
+
+
+def control_queue_from_config(config):
+ """
+ Returns a Queue instance with the correct name and routing key for this
+ galaxy process's config
+ """
+ return Queue("control.%s" % config.server_name, galaxy_exchange,
+ routing_key='control')
diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/web/base/controllers/admin.py
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -5,6 +5,7 @@
from galaxy.util import inflector
from galaxy.web.form_builder import CheckboxField
from string import punctuation as PUNCTUATION
+import galaxy.queue_worker
log = logging.getLogger( __name__ )
@@ -62,8 +63,9 @@
toolbox = self.app.toolbox
tool_id = None
if params.get( 'reload_tool_button', False ):
- tool_id = params.tool_id
- message, status = toolbox.reload_tool_by_id( tool_id )
+ tool_id = params.get('tool_id', None)
+ galaxy.queue_worker.send_control_task(trans, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id} )
+ message, status = trans.app.toolbox.reload_tool_by_id( tool_id)
return trans.fill_template( '/admin/reload_tool.mako',
tool_id=tool_id,
toolbox=toolbox,
diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 lib/galaxy/webapps/galaxy/controllers/data_manager.py
--- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py
+++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
@@ -1,6 +1,7 @@
+import galaxy.queue_worker
from galaxy import web
+from galaxy.util.json import from_json_string
from galaxy.web.base.controller import BaseUIController
-from galaxy.util.json import from_json_string
import pkg_resources;
pkg_resources.require( "Paste" )
@@ -90,6 +91,9 @@
table_name = table_name.split( "," )
# Reload the tool data tables
table_names = self.app.tool_data_tables.reload_tables( table_names=table_name )
+ galaxy.queue_worker.send_control_task(trans, 'reload_tool_data_tables',
+ noop_self=True,
+ kwargs={'table_name': table_name} )
redirect_url = None
if table_names:
status = 'done'
diff -r da128dd1ab03d905da0cf8dafec70443267cff64 -r c822084e6e5407c6ac80f999fa313808049e58f7 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -821,7 +821,21 @@
#user_tool_section_filters = examples:restrict_text
#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode
-# ---- Galaxy Message Queue -------------------------------------------------
+# Galaxy Application Internal Message Queue
+
+# Galaxy uses AMQP internally TODO more documentation on what for.
+# For examples, see http://ask.github.io/kombu/userguide/connections.html
+#
+# Without specifying anything here, galaxy will first attempt to use your
+# specified database_connection above. If that's not specified either, Galaxy
+# will automatically create and use a separate sqlite database located in your
+# <galaxy>/database folder (indicated in the commented out line below).
+
+#amqp_internal_connection = "sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE"
+
+
+
+# ---- Galaxy External Message Queue -------------------------------------------------
# Galaxy uses AMQ protocol to receive messages from external sources like
# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/da128dd1ab03/
Changeset: da128dd1ab03
Branch: next-stable
User: davebgx
Date: 2014-05-19 22:38:58
Summary: Remove migrated tools from main's tool_conf.xml
Affected #: 1 file
diff -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 -r da128dd1ab03d905da0cf8dafec70443267cff64 tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -41,12 +41,10 @@
</section><section id="convert" name="Convert Formats"><tool file="filters/bed2gff.xml" />
- <tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" /><tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" />
- <tool file="fasta_tools/tabular_to_fasta.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" />
https://bitbucket.org/galaxy/galaxy-central/commits/174b6a2281e5/
Changeset: 174b6a2281e5
User: davebgx
Date: 2014-05-19 22:39:25
Summary: Merge with next-stable.
Affected #: 1 file
diff -r 9b33b543fb1448f8f775ac975e2605ac610c8f63 -r 174b6a2281e53793a8188ba2b2792d0dd220d362 tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -41,12 +41,10 @@
</section><section id="convert" name="Convert Formats"><tool file="filters/bed2gff.xml" />
- <tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" /><tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" />
- <tool file="fasta_tools/tabular_to_fasta.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
commit/galaxy-central: natefoo: Open next-stable for upcoming June release.
by commits-noreply＠bitbucket.org 19 May '14
by commits-noreply＠bitbucket.org 19 May '14
19 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9ebe5ccabe02/
Changeset: 9ebe5ccabe02
Branch: next-stable
User: natefoo
Date: 2014-05-19 21:55:21
Summary: Open next-stable for upcoming June release.
Affected #: 740 files
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -6,3 +6,4 @@
1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12
26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04
5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10
+9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/app.css
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/app.css
@@ -0,0 +1,67 @@
+.charts-grid .item {
+ padding: 5px;
+ margin: 5px;
+ float: left;
+ cursor: pointer;
+ border-radius:5px
+}
+
+.charts-grid .current {
+ border-color:#66afe9;
+ background-color:#EEEEFF;
+ outline:0;
+ -webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
+ box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
+}
+
+.charts-grid .image {
+ padding: 10px;
+ width: 100px;
+}
+
+.charts-grid .title {
+ text-align: center;
+ font-size: 0.9em;
+ word-wrap: break-work;
+ font-weight: bold;
+ width: 100px;
+}
+
+.charts-grid .header {
+ font-size: 0.9em;
+ font-weight: bold;
+}
+
+.charts-viewport {
+ height: inherit;
+ min-height: 50px;
+}
+
+.charts-viewport .info {
+ position: absolute;
+ margin: 10px 20px 50px 10px;
+}
+
+.charts-viewport .text {
+ position: relative;
+ margin-left: 5px;
+ top: -1px;
+ font-size: 1.0em;
+}
+
+.charts-viewport .icon {
+ font-size: 1.2em;
+ display: inline-block;
+}
+
+.charts-viewport .charts-viewport-container {
+ float: left;
+ display: block;
+ height: 100%;
+}
+
+.charts-viewport .charts-viewport-canvas {
+ display: block;
+ width:100%;
+ height: inherit;
+}
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -51,7 +51,7 @@
// append views
this.$el.append(this.viewer_view.$el);
this.$el.append(this.editor_view.$el);
-
+
// pick start screen
if (!this.storage.load()) {
// show editor
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-(function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof x)return e;if(!(this instanceof x))return new x(e);this._wrapped=e};typeof exports!="undefined"?(typeof module!="undefined"&&module.exports&&(exports=module.exports=x),exports._=x):e._=x,x.VERSION="1.4.4";var T=x.each=x.forEach=function(e,t,r){if(e==null)return;if(c&&e.forEach===c)e.forEach(t,r);else if(e.length===+e.length){for(var i=0,s=e.length;i<s;i++)if(t.call(r,e[i],i,e)===n)return}else for(var o in e)if(x.has(e,o)&&t.call(r,e[o],o,e)===n)return};x.map=x.collect=function(e,t,n){var r=[];return e==null?r:h&&e.map===h?e.map(t,n):(T(e,function(e,i,s){r.push(t.call(n,e,i,s))}),r)};var N="Reduce of empty array with no initial value";x.reduce=x.foldl=x.inject=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(p&&e.reduce===p)return r&&(t=x.bind(t,r)),i?e.reduce(t,n):e.reduce(t);T(e,function(e,s,o){i?n=t.call(r,n,e,s,o):(n=e,i=!0)});if(!i)throw new TypeError(N);return n},x.reduceRight=x.foldr=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(d&&e.reduceRight===d)return r&&(t=x.bind(t,r)),i?e.reduceRight(t,n):e.reduceRight(t);var s=e.length;if(s!==+s){var o=x.keys(e);s=o.length}T(e,function(u,a,f){a=o?o[--s]:--s,i?n=t.call(r,n,e[a],a,f):(n=e[a],i=!0)});if(!i)throw new TypeError(N);return n},x.find=x.detect=function(e,t,n){var r;return C(e,function(e,i,s){if(t.call(n,e,i,s))return r=e,!0}),r},x.filter=x.select=function(e,t,n){var r=[];return e==null?r:v&&e.filter===v?e.filter(t,n):(T(e,function(e,i,s){t.call(n,e,i,s)&&r.push(e)}),r)},x.reject=function(e,t,n){return x.filter(e,function(e,r,i){return!t.call(n,e,r,i)},n)},x.every=x.all=function(e,t,r){t||(t=x.identity);var i=!0;return e==null?i:m&&e.every===m?e.every(t,r):(T(e,function(e,s,o){if(!(i=i&&t.call(r,e,s,o)))return n}),!!i)};var C=x.some=x.any=function(e,t,r){t||(t=x.identity);var i=!1;return e==null?i:g&&e.some===g?e.some(t,r):(T(e,function(e,s,o){if(i||(i=t.call(r,e,s,o)))return n}),!!i)};x.contains=x.include=function(e,t){return e==null?!1:y&&e.indexOf===y?e.indexOf(t)!=-1:C(e,function(e){return e===t})},x.invoke=function(e,t){var n=u.call(arguments,2),r=x.isFunction(t);return x.map(e,function(e){return(r?t:e[t]).apply(e,n)})},x.pluck=function(e,t){return x.map(e,function(e){return e[t]})},x.where=function(e,t,n){return x.isEmpty(t)?n?void 0:[]:x[n?"find":"filter"](e,function(e){for(var n in t)if(t[n]!==e[n])return!1;return!0})},x.findWhere=function(e,t){return x.where(e,t,!0)},x.max=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.max.apply(Math,e);if(!t&&x.isEmpty(e))return-Infinity;var r={computed:-Infinity,value:-Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o>=r.computed&&(r={value:e,computed:o})}),r.value},x.min=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.min.apply(Math,e);if(!t&&x.isEmpty(e))return Infinity;var r={computed:Infinity,value:Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o<r.computed&&(r={value:e,computed:o})}),r.value},x.shuffle=function(e){var t,n=0,r=[];return T(e,function(e){t=x.random(n++),r[n-1]=r[t],r[t]=e}),r};var k=function(e){return x.isFunction(e)?e:function(t){return t[e]}};x.sortBy=function(e,t,n){var r=k(t);return x.pluck(x.map(e,function(e,t,i){return{value:e,index:t,criteria:r.call(n,e,t,i)}}).sort(function(e,t){var n=e.criteria,r=t.criteria;if(n!==r){if(n>r||n===void 0)return 1;if(n<r||r===void 0)return-1}return e.index<t.index?-1:1}),"value")};var L=function(e,t,n,r){var i={},s=k(t==null?x.identity:t);return T(e,function(t,o){var u=s.call(n,t,o,e);r(i,u,t)}),i};x.groupBy=function(e,t,n){return L(e,t,n,function(e,t,n){(x.has(e,t)?e[t]:e[t]=[]).push(n)})},x.countBy=function(e,t,n){return L(e,t,n,function(e,t){x.has(e,t)||(e[t]=0),e[t]++})},x.sortedIndex=function(e,t,n,r){n=n==null?x.identity:k(n);var i=n.call(r,t),s=0,o=e.length;while(s<o){var u=s+o>>>1;n.call(r,e[u])<i?s=u+1:o=u}return s},x.toArray=function(e){return e?x.isArray(e)?u.call(e):e.length===+e.length?x.map(e,x.identity):x.values(e):[]},x.size=function(e){return e==null?0:e.length===+e.length?e.length:x.keys(e).length},x.first=x.head=x.take=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,0,t):e[0]},x.initial=function(e,t,n){return u.call(e,0,e.length-(t==null||n?1:t))},x.last=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,Math.max(e.length-t,0)):e[e.length-1]},x.rest=x.tail=x.drop=function(e,t,n){return u.call(e,t==null||n?1:t)},x.compact=function(e){return x.filter(e,x.identity)};var A=function(e,t,n){return T(e,function(e){x.isArray(e)?t?o.apply(n,e):A(e,t,n):n.push(e)}),n};x.flatten=function(e,t){return A(e,t,[])},x.without=function(e){return x.difference(e,u.call(arguments,1))},x.uniq=x.unique=function(e,t,n,r){x.isFunction(t)&&(r=n,n=t,t=!1);var i=n?x.map(e,n,r):e,s=[],o=[];return T(i,function(n,r){if(t?!r||o[o.length-1]!==n:!x.contains(o,n))o.push(n),s.push(e[r])}),s},x.union=function(){return x.uniq(a.apply(r,arguments))},x.intersection=function(e){var t=u.call(arguments,1);return x.filter(x.uniq(e),function(e){return x.every(t,function(t){return x.indexOf(t,e)>=0})})},x.difference=function(e){var t=a.apply(r,u.call(arguments,1));return x.filter(e,function(e){return!x.contains(t,e)})},x.zip=function(){var e=u.call(arguments),t=x.max(x.pluck(e,"length")),n=new Array(t);for(var r=0;r<t;r++)n[r]=x.pluck(e,""+r);return n},x.unzip=function(e){var t=[];return x.each(e,function(e,n){x.each(e,function(e,r){t.length<=r&&(t[r]=[]),t[r][n]=e})}),t},x.object=function(e,t){if(e==null)return{};var n={};for(var r=0,i=e.length;r<i;r++)t?n[e[r]]=t[r]:n[e[r][0]]=e[r][1];return n},x.indexOf=function(e,t,n){if(e==null)return-1;var r=0,i=e.length;if(n){if(typeof n!="number")return r=x.sortedIndex(e,t),e[r]===t?r:-1;r=n<0?Math.max(0,i+n):n}if(y&&e.indexOf===y)return e.indexOf(t,n);for(;r<i;r++)if(e[r]===t)return r;return-1},x.lastIndexOf=function(e,t,n){if(e==null)return-1;var r=n!=null;if(b&&e.lastIndexOf===b)return r?e.lastIndexOf(t,n):e.lastIndexOf(t);var i=r?n:e.length;while(i--)if(e[i]===t)return i;return-1},x.range=function(e,t,n){arguments.length<=1&&(t=e||0,e=0),n=arguments[2]||1;var r=Math.max(Math.ceil((t-e)/n),0),i=0,s=new Array(r);while(i<r)s[i++]=e,e+=n;return s};var O=function(){};x.bind=function(e,t){var n,r;if(e.bind===S&&S)return S.apply(e,u.call(arguments,1));if(!x.isFunction(e))throw new TypeError;return n=u.call(arguments,2),r=function(){if(this instanceof r){O.prototype=e.prototype;var i=new O;O.prototype=null;var s=e.apply(i,n.concat(u.call(arguments)));return Object(s)===s?s:i}return e.apply(t,n.concat(u.call(arguments)))}},x.partial=function(e){var t=u.call(arguments,1);return function(){return e.apply(this,t.concat(u.call(arguments)))}},x.bindAll=function(e){var t=u.call(arguments,1);if(t.length===0)throw new Error("bindAll must be passed function names");return T(t,function(t){e[t]=x.bind(e[t],e)}),e},x.memoize=function(e,t){var n={};return t||(t=x.identity),function(){var r=t.apply(this,arguments);return x.has(n,r)?n[r]:n[r]=e.apply(this,arguments)}},x.delay=function(e,t){var n=u.call(arguments,2);return setTimeout(function(){return e.apply(null,n)},t)},x.defer=function(e){return x.delay.apply(x,[e,1].concat(u.call(arguments,1)))},x.throttle=function(e,t,n){var r,i,s,o,u=0,a=function(){u=new Date,s=null,o=e.apply(r,i)};return function(){var f=new Date;!u&&n===!1&&(u=f);var l=t-(f-u);return r=this,i=arguments,l<=0?(clearTimeout(s),s=null,u=f,o=e.apply(r,i)):s||(s=setTimeout(a,l)),o}},x.debounce=function(e,t,n){var r,i;return function(){var s=this,o=arguments,u=function(){r=null,n||(i=e.apply(s,o))},a=n&&!r;return clearTimeout(r),r=setTimeout(u,t),a&&(i=e.apply(s,o)),i}},x.once=function(e){var t=!1,n;return function(){return t?n:(t=!0,n=e.apply(this,arguments),e=null,n)}},x.wrap=function(e,t){return function(){var n=[e];return o.apply(n,arguments),t.apply(this,n)}},x.compose=function(){var e=arguments;return function(){var t=arguments;for(var n=e.length-1;n>=0;n--)t=[e[n].apply(this,t)];return t[0]}},x.after=function(e,t){return e<=0?t():function(){if(--e<1)return t.apply(this,arguments)}},x.keys=E||function(e){if(e!==Object(e))throw new TypeError("Invalid object");var t=[];for(var n in e)x.has(e,n)&&t.push(n);return t},x.values=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push(e[n]);return t},x.pairs=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push([n,e[n]]);return t},x.invert=function(e){var t={};for(var n in e)x.has(e,n)&&(t[e[n]]=n);return t},x.functions=x.methods=function(e){var t=[];for(var n in e)x.isFunction(e[n])&&t.push(n);return t.sort()},x.extend=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]=t[n]}),e},x.pick=function(e){var t={},n=a.apply(r,u.call(arguments,1));return T(n,function(n){n in e&&(t[n]=e[n])}),t},x.omit=function(e){var t={},n=a.apply(r,u.call(arguments,1));for(var i in e)x.contains(n,i)||(t[i]=e[i]);return t},x.defaults=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]===void 0&&(e[n]=t[n])}),e},x.clone=function(e){return x.isObject(e)?x.isArray(e)?e.slice():x.extend({},e):e},x.tap=function(e,t){return t(e),e};var M=function(e,t,n,r){if(e===t)return e!==0||1/e==1/t;if(e==null||t==null)return e===t;e instanceof x&&(e=e._wrapped),t instanceof x&&(t=t._wrapped);var i=f.call(e);if(i!=f.call(t))return!1;switch(i){case"[object String]":return e==String(t);case"[object Number]":return e!=+e?t!=+t:e==0?1/e==1/t:e==+t;case"[object Date]":case"[object Boolean]":return+e==+t;case"[object RegExp]":return e.source==t.source&&e.global==t.global&&e.multiline==t.multiline&&e.ignoreCase==t.ignoreCase}if(typeof e!="object"||typeof t!="object")return!1;var s=n.length;while(s--)if(n[s]==e)return r[s]==t;n.push(e),r.push(t);var o=0,u=!0;if(i=="[object Array]"){o=e.length,u=o==t.length;if(u)while(o--)if(!(u=M(e[o],t[o],n,r)))break}else{var a=e.constructor,l=t.constructor;if(a!==l&&!(x.isFunction(a)&&a instanceof a&&x.isFunction(l)&&l instanceof l))return!1;for(var c in e)if(x.has(e,c)){o++;if(!(u=x.has(t,c)&&M(e[c],t[c],n,r)))break}if(u){for(c in t)if(x.has(t,c)&&!(o--))break;u=!o}}return n.pop(),r.pop(),u};x.isEqual=function(e,t){return M(e,t,[],[])},x.isEmpty=function(e){if(e==null)return!0;if(x.isArray(e)||x.isString(e))return e.length===0;for(var t in e)if(x.has(e,t))return!1;return!0},x.isElement=function(e){return!!e&&e.nodeType===1},x.isArray=w||function(e){return f.call(e)=="[object Array]"},x.isObject=function(e){return e===Object(e)},T(["Arguments","Function","String","Number","Date","RegExp"],function(e){x["is"+e]=function(t){return f.call(t)=="[object "+e+"]"}}),x.isArguments(arguments)||(x.isArguments=function(e){return!!e&&!!x.has(e,"callee")}),typeof /./!="function"&&(x.isFunction=function(e){return typeof e=="function"}),x.isFinite=function(e){return isFinite(e)&&!isNaN(parseFloat(e))},x.isNaN=function(e){return x.isNumber(e)&&e!=+e},x.isBoolean=function(e){return e===!0||e===!1||f.call(e)=="[object Boolean]"},x.isNull=function(e){return e===null},x.isUndefined=function(e){return e===void 0},x.has=function(e,t){return l.call(e,t)},x.noConflict=function(){return e._=t,this},x.identity=function(e){return e},x.times=function(e,t,n){var r=Array(e);for(var i=0;i<e;i++)r[i]=t.call(n,i);return r},x.random=function(e,t){return t==null&&(t=e,e=0),e+Math.floor(Math.random()*(t-e+1))};var _={escape:{"&":"&","<":"<",">":">",'"':""","'":"'","/":"/"}};_.unescape=x.invert(_.escape);var D={escape:new RegExp("["+x.keys(_.escape).join("")+"]","g"),unescape:new RegExp("("+x.keys(_.unescape).join("|")+")","g")};x.each(["escape","unescape"],function(e){x[e]=function(t){return t==null?"":(""+t).replace(D[e],function(t){return _[e][t]})}}),x.result=function(e,t){if(e==null)return void 0;var n=e[t];return x.isFunction(n)?n.call(e):n},x.mixin=function(e){T(x.functions(e),function(t){var n=x[t]=e[t];x.prototype[t]=function(){var e=[this._wrapped];return o.apply(e,arguments),F.call(this,n.apply(x,e))}})};var P=0;x.uniqueId=function(e){var t=++P+"";return e?e+t:t},x.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var H=/(.)^/,B={"'":"'","\\":"\\","\r":"r","\n":"n"," ":"t","\u2028":"u2028","\u2029":"u2029"},j=/\\|'|\r|\n|\t|\u2028|\u2029/g;x.template=function(e,t,n){var r;n=x.defaults({},n,x.templateSettings);var i=new RegExp([(n.escape||H).source,(n.interpolate||H).source,(n.evaluate||H).source].join("|")+"|$","g"),s=0,o="__p+='";e.replace(i,function(t,n,r,i,u){return o+=e.slice(s,u).replace(j,function(e){return"\\"+B[e]}),n&&(o+="'+\n((__t=("+n+"))==null?'':_.escape(__t))+\n'"),r&&(o+="'+\n((__t=("+r+"))==null?'':__t)+\n'"),i&&(o+="';\n"+i+"\n__p+='"),s=u+t.length,t}),o+="';\n",n.variable||(o="with(obj||{}){\n"+o+"}\n"),o="var __t,__p='',__j=Array.prototype.join,print=function(){__p+=__j.call(arguments,'');};\n"+o+"return __p;\n";try{r=new Function(n.variable||"obj","_",o)}catch(u){throw u.source=o,u}if(t)return r(t,x);var a=function(e){return r.call(this,e,x)};return a.source="function("+(n.variable||"obj")+"){\n"+o+"}",a},x.chain=function(e){return x(e).chain()};var F=function(e){return this._chain?x(e).chain():e};x.mixin(x),T(["pop","push","reverse","shift","sort","splice","unshift"],function(e){var t=r[e];x.prototype[e]=function(){var n=this._wrapped;return t.apply(n,arguments),(e=="shift"||e=="splice")&&n.length===0&&delete n[0],F.call(this,n)}}),T(["concat","join","slice"],function(e){var t=r[e];x.prototype[e]=function(){return F.call(this,t.apply(this._wrapped,arguments))}}),x.extend(x.prototype,{chain:function(){return this._chain=!0,this},value:function(){return this._wrapped}})}).call(this),define("libs/underscore",function(e){return function(){var t,n;return t||e._}}(this)),define("utils/utils",["libs/underscore"],function(e){function t(e,t,r){n("GET",e,{},t,r)}function n(e,t,n,r,i){if(e=="GET"||e=="DELETE")t.indexOf("?")==-1?t+="?":t+="&",t+=$.param(n);var s=new XMLHttpRequest;s.open(e,t,!0),s.setRequestHeader("Accept","application/json"),s.setRequestHeader("Cache-Control","no-cache"),s.setRequestHeader("X-Requested-With","XMLHttpRequest"),s.setRequestHeader("Content-Type","application/json"),s.onloadend=function(){var e=s.status;try{response=jQuery.parseJSON(s.responseText)}catch(t){response=s.responseText}e==200?r&&r(response):i&&i(response)},e=="GET"||e=="DELETE"?s.send():s.send(JSON.stringify(n))}function r(e,t){var n=$('<div class="'+e+'"></div>');n.appendTo(":eq(0)");var r=n.css(t);return n.remove(),r}function i(e){$('link[href^="'+e+'"]').length||$('<link href="'+galaxy_config.root+e+'" rel="stylesheet">').appendTo("head")}function s(t,n){return t?e.defaults(t,n):n}function o(e,t){var n="";if(e>=1e11)e/=1e11,n="TB";else if(e>=1e8)e/=1e8,n="GB";else if(e>=1e5)e/=1e5,n="MB";else if(e>=100)e/=100,n="KB";else{if(!(e>0))return"<strong>-</strong>";e*=10,n="b"}var r=Math.round(e)/10;return t?r+" "+n:"<strong>"+r+"</strong> "+n}function u(){return(new Date).getTime().toString(36)}function a(e){var t=$("<p></p>");return t.append(e),t}function f(){var e=new Date,t=(e.getHours()<10?"0":"")+e.getHours(),n=(e.getMinutes()<10?"0":"")+e.getMinutes(),r=e.getDate()+"/"+(e.getMonth()+1)+"/"+e.getFullYear()+", "+t+":"+n;return r}return{cssLoadFile:i,cssGetAttribute:r,get:t,merge:s,bytesToString:o,uuid:u,time:f,wrap:a,request:n}}),define("mvc/ui/ui-modal",["utils/utils"],function(e){var t=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast")},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:a,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._create_svg();var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg_el=this.$el.find("svg"),this.svg=d3.select(this.svg_el[0])},_draw:function(e){var t=this;this._create_svg(),e.state("wait","Please wait...");var n=e.deferred.register(),r=e.get("type"),i=this.app.types.get(r);if(!i.execute||i.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var s=new r(t.app,{svg:t.svg});i.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){s.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):s.draw(n,e,t._defaultRequestDictionary(e)):s.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
+define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof x)return e;if(!(this instanceof x))return new x(e);this._wrapped=e};typeof exports!="undefined"?(typeof module!="undefined"&&module.exports&&(exports=module.exports=x),exports._=x):e._=x,x.VERSION="1.4.4";var T=x.each=x.forEach=function(e,t,r){if(e==null)return;if(c&&e.forEach===c)e.forEach(t,r);else if(e.length===+e.length){for(var i=0,s=e.length;i<s;i++)if(t.call(r,e[i],i,e)===n)return}else for(var o in e)if(x.has(e,o)&&t.call(r,e[o],o,e)===n)return};x.map=x.collect=function(e,t,n){var r=[];return e==null?r:h&&e.map===h?e.map(t,n):(T(e,function(e,i,s){r.push(t.call(n,e,i,s))}),r)};var N="Reduce of empty array with no initial value";x.reduce=x.foldl=x.inject=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(p&&e.reduce===p)return r&&(t=x.bind(t,r)),i?e.reduce(t,n):e.reduce(t);T(e,function(e,s,o){i?n=t.call(r,n,e,s,o):(n=e,i=!0)});if(!i)throw new TypeError(N);return n},x.reduceRight=x.foldr=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(d&&e.reduceRight===d)return r&&(t=x.bind(t,r)),i?e.reduceRight(t,n):e.reduceRight(t);var s=e.length;if(s!==+s){var o=x.keys(e);s=o.length}T(e,function(u,a,f){a=o?o[--s]:--s,i?n=t.call(r,n,e[a],a,f):(n=e[a],i=!0)});if(!i)throw new TypeError(N);return n},x.find=x.detect=function(e,t,n){var r;return C(e,function(e,i,s){if(t.call(n,e,i,s))return r=e,!0}),r},x.filter=x.select=function(e,t,n){var r=[];return e==null?r:v&&e.filter===v?e.filter(t,n):(T(e,function(e,i,s){t.call(n,e,i,s)&&r.push(e)}),r)},x.reject=function(e,t,n){return x.filter(e,function(e,r,i){return!t.call(n,e,r,i)},n)},x.every=x.all=function(e,t,r){t||(t=x.identity);var i=!0;return e==null?i:m&&e.every===m?e.every(t,r):(T(e,function(e,s,o){if(!(i=i&&t.call(r,e,s,o)))return n}),!!i)};var C=x.some=x.any=function(e,t,r){t||(t=x.identity);var i=!1;return e==null?i:g&&e.some===g?e.some(t,r):(T(e,function(e,s,o){if(i||(i=t.call(r,e,s,o)))return n}),!!i)};x.contains=x.include=function(e,t){return e==null?!1:y&&e.indexOf===y?e.indexOf(t)!=-1:C(e,function(e){return e===t})},x.invoke=function(e,t){var n=u.call(arguments,2),r=x.isFunction(t);return x.map(e,function(e){return(r?t:e[t]).apply(e,n)})},x.pluck=function(e,t){return x.map(e,function(e){return e[t]})},x.where=function(e,t,n){return x.isEmpty(t)?n?void 0:[]:x[n?"find":"filter"](e,function(e){for(var n in t)if(t[n]!==e[n])return!1;return!0})},x.findWhere=function(e,t){return x.where(e,t,!0)},x.max=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.max.apply(Math,e);if(!t&&x.isEmpty(e))return-Infinity;var r={computed:-Infinity,value:-Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o>=r.computed&&(r={value:e,computed:o})}),r.value},x.min=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.min.apply(Math,e);if(!t&&x.isEmpty(e))return Infinity;var r={computed:Infinity,value:Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o<r.computed&&(r={value:e,computed:o})}),r.value},x.shuffle=function(e){var t,n=0,r=[];return T(e,function(e){t=x.random(n++),r[n-1]=r[t],r[t]=e}),r};var k=function(e){return x.isFunction(e)?e:function(t){return t[e]}};x.sortBy=function(e,t,n){var r=k(t);return x.pluck(x.map(e,function(e,t,i){return{value:e,index:t,criteria:r.call(n,e,t,i)}}).sort(function(e,t){var n=e.criteria,r=t.criteria;if(n!==r){if(n>r||n===void 0)return 1;if(n<r||r===void 0)return-1}return e.index<t.index?-1:1}),"value")};var L=function(e,t,n,r){var i={},s=k(t==null?x.identity:t);return T(e,function(t,o){var u=s.call(n,t,o,e);r(i,u,t)}),i};x.groupBy=function(e,t,n){return L(e,t,n,function(e,t,n){(x.has(e,t)?e[t]:e[t]=[]).push(n)})},x.countBy=function(e,t,n){return L(e,t,n,function(e,t){x.has(e,t)||(e[t]=0),e[t]++})},x.sortedIndex=function(e,t,n,r){n=n==null?x.identity:k(n);var i=n.call(r,t),s=0,o=e.length;while(s<o){var u=s+o>>>1;n.call(r,e[u])<i?s=u+1:o=u}return s},x.toArray=function(e){return e?x.isArray(e)?u.call(e):e.length===+e.length?x.map(e,x.identity):x.values(e):[]},x.size=function(e){return e==null?0:e.length===+e.length?e.length:x.keys(e).length},x.first=x.head=x.take=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,0,t):e[0]},x.initial=function(e,t,n){return u.call(e,0,e.length-(t==null||n?1:t))},x.last=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,Math.max(e.length-t,0)):e[e.length-1]},x.rest=x.tail=x.drop=function(e,t,n){return u.call(e,t==null||n?1:t)},x.compact=function(e){return x.filter(e,x.identity)};var A=function(e,t,n){return T(e,function(e){x.isArray(e)?t?o.apply(n,e):A(e,t,n):n.push(e)}),n};x.flatten=function(e,t){return A(e,t,[])},x.without=function(e){return x.difference(e,u.call(arguments,1))},x.uniq=x.unique=function(e,t,n,r){x.isFunction(t)&&(r=n,n=t,t=!1);var i=n?x.map(e,n,r):e,s=[],o=[];return T(i,function(n,r){if(t?!r||o[o.length-1]!==n:!x.contains(o,n))o.push(n),s.push(e[r])}),s},x.union=function(){return x.uniq(a.apply(r,arguments))},x.intersection=function(e){var t=u.call(arguments,1);return x.filter(x.uniq(e),function(e){return x.every(t,function(t){return x.indexOf(t,e)>=0})})},x.difference=function(e){var t=a.apply(r,u.call(arguments,1));return x.filter(e,function(e){return!x.contains(t,e)})},x.zip=function(){var e=u.call(arguments),t=x.max(x.pluck(e,"length")),n=new Array(t);for(var r=0;r<t;r++)n[r]=x.pluck(e,""+r);return n},x.unzip=function(e){var t=[];return x.each(e,function(e,n){x.each(e,function(e,r){t.length<=r&&(t[r]=[]),t[r][n]=e})}),t},x.object=function(e,t){if(e==null)return{};var n={};for(var r=0,i=e.length;r<i;r++)t?n[e[r]]=t[r]:n[e[r][0]]=e[r][1];return n},x.indexOf=function(e,t,n){if(e==null)return-1;var r=0,i=e.length;if(n){if(typeof n!="number")return r=x.sortedIndex(e,t),e[r]===t?r:-1;r=n<0?Math.max(0,i+n):n}if(y&&e.indexOf===y)return e.indexOf(t,n);for(;r<i;r++)if(e[r]===t)return r;return-1},x.lastIndexOf=function(e,t,n){if(e==null)return-1;var r=n!=null;if(b&&e.lastIndexOf===b)return r?e.lastIndexOf(t,n):e.lastIndexOf(t);var i=r?n:e.length;while(i--)if(e[i]===t)return i;return-1},x.range=function(e,t,n){arguments.length<=1&&(t=e||0,e=0),n=arguments[2]||1;var r=Math.max(Math.ceil((t-e)/n),0),i=0,s=new Array(r);while(i<r)s[i++]=e,e+=n;return s};var O=function(){};x.bind=function(e,t){var n,r;if(e.bind===S&&S)return S.apply(e,u.call(arguments,1));if(!x.isFunction(e))throw new TypeError;return n=u.call(arguments,2),r=function(){if(this instanceof r){O.prototype=e.prototype;var i=new O;O.prototype=null;var s=e.apply(i,n.concat(u.call(arguments)));return Object(s)===s?s:i}return e.apply(t,n.concat(u.call(arguments)))}},x.partial=function(e){var t=u.call(arguments,1);return function(){return e.apply(this,t.concat(u.call(arguments)))}},x.bindAll=function(e){var t=u.call(arguments,1);if(t.length===0)throw new Error("bindAll must be passed function names");return T(t,function(t){e[t]=x.bind(e[t],e)}),e},x.memoize=function(e,t){var n={};return t||(t=x.identity),function(){var r=t.apply(this,arguments);return x.has(n,r)?n[r]:n[r]=e.apply(this,arguments)}},x.delay=function(e,t){var n=u.call(arguments,2);return setTimeout(function(){return e.apply(null,n)},t)},x.defer=function(e){return x.delay.apply(x,[e,1].concat(u.call(arguments,1)))},x.throttle=function(e,t,n){var r,i,s,o,u=0,a=function(){u=new Date,s=null,o=e.apply(r,i)};return function(){var f=new Date;!u&&n===!1&&(u=f);var l=t-(f-u);return r=this,i=arguments,l<=0?(clearTimeout(s),s=null,u=f,o=e.apply(r,i)):s||(s=setTimeout(a,l)),o}},x.debounce=function(e,t,n){var r,i;return function(){var s=this,o=arguments,u=function(){r=null,n||(i=e.apply(s,o))},a=n&&!r;return clearTimeout(r),r=setTimeout(u,t),a&&(i=e.apply(s,o)),i}},x.once=function(e){var t=!1,n;return function(){return t?n:(t=!0,n=e.apply(this,arguments),e=null,n)}},x.wrap=function(e,t){return function(){var n=[e];return o.apply(n,arguments),t.apply(this,n)}},x.compose=function(){var e=arguments;return function(){var t=arguments;for(var n=e.length-1;n>=0;n--)t=[e[n].apply(this,t)];return t[0]}},x.after=function(e,t){return e<=0?t():function(){if(--e<1)return t.apply(this,arguments)}},x.keys=E||function(e){if(e!==Object(e))throw new TypeError("Invalid object");var t=[];for(var n in e)x.has(e,n)&&t.push(n);return t},x.values=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push(e[n]);return t},x.pairs=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push([n,e[n]]);return t},x.invert=function(e){var t={};for(var n in e)x.has(e,n)&&(t[e[n]]=n);return t},x.functions=x.methods=function(e){var t=[];for(var n in e)x.isFunction(e[n])&&t.push(n);return t.sort()},x.extend=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]=t[n]}),e},x.pick=function(e){var t={},n=a.apply(r,u.call(arguments,1));return T(n,function(n){n in e&&(t[n]=e[n])}),t},x.omit=function(e){var t={},n=a.apply(r,u.call(arguments,1));for(var i in e)x.contains(n,i)||(t[i]=e[i]);return t},x.defaults=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]===void 0&&(e[n]=t[n])}),e},x.clone=function(e){return x.isObject(e)?x.isArray(e)?e.slice():x.extend({},e):e},x.tap=function(e,t){return t(e),e};var M=function(e,t,n,r){if(e===t)return e!==0||1/e==1/t;if(e==null||t==null)return e===t;e instanceof x&&(e=e._wrapped),t instanceof x&&(t=t._wrapped);var i=f.call(e);if(i!=f.call(t))return!1;switch(i){case"[object String]":return e==String(t);case"[object Number]":return e!=+e?t!=+t:e==0?1/e==1/t:e==+t;case"[object Date]":case"[object Boolean]":return+e==+t;case"[object RegExp]":return e.source==t.source&&e.global==t.global&&e.multiline==t.multiline&&e.ignoreCase==t.ignoreCase}if(typeof e!="object"||typeof t!="object")return!1;var s=n.length;while(s--)if(n[s]==e)return r[s]==t;n.push(e),r.push(t);var o=0,u=!0;if(i=="[object Array]"){o=e.length,u=o==t.length;if(u)while(o--)if(!(u=M(e[o],t[o],n,r)))break}else{var a=e.constructor,l=t.constructor;if(a!==l&&!(x.isFunction(a)&&a instanceof a&&x.isFunction(l)&&l instanceof l))return!1;for(var c in e)if(x.has(e,c)){o++;if(!(u=x.has(t,c)&&M(e[c],t[c],n,r)))break}if(u){for(c in t)if(x.has(t,c)&&!(o--))break;u=!o}}return n.pop(),r.pop(),u};x.isEqual=function(e,t){return M(e,t,[],[])},x.isEmpty=function(e){if(e==null)return!0;if(x.isArray(e)||x.isString(e))return e.length===0;for(var t in e)if(x.has(e,t))return!1;return!0},x.isElement=function(e){return!!e&&e.nodeType===1},x.isArray=w||function(e){return f.call(e)=="[object Array]"},x.isObject=function(e){return e===Object(e)},T(["Arguments","Function","String","Number","Date","RegExp"],function(e){x["is"+e]=function(t){return f.call(t)=="[object "+e+"]"}}),x.isArguments(arguments)||(x.isArguments=function(e){return!!e&&!!x.has(e,"callee")}),typeof /./!="function"&&(x.isFunction=function(e){return typeof e=="function"}),x.isFinite=function(e){return isFinite(e)&&!isNaN(parseFloat(e))},x.isNaN=function(e){return x.isNumber(e)&&e!=+e},x.isBoolean=function(e){return e===!0||e===!1||f.call(e)=="[object Boolean]"},x.isNull=function(e){return e===null},x.isUndefined=function(e){return e===void 0},x.has=function(e,t){return l.call(e,t)},x.noConflict=function(){return e._=t,this},x.identity=function(e){return e},x.times=function(e,t,n){var r=Array(e);for(var i=0;i<e;i++)r[i]=t.call(n,i);return r},x.random=function(e,t){return t==null&&(t=e,e=0),e+Math.floor(Math.random()*(t-e+1))};var _={escape:{"&":"&","<":"<",">":">",'"':""","'":"'","/":"/"}};_.unescape=x.invert(_.escape);var D={escape:new RegExp("["+x.keys(_.escape).join("")+"]","g"),unescape:new RegExp("("+x.keys(_.unescape).join("|")+")","g")};x.each(["escape","unescape"],function(e){x[e]=function(t){return t==null?"":(""+t).replace(D[e],function(t){return _[e][t]})}}),x.result=function(e,t){if(e==null)return void 0;var n=e[t];return x.isFunction(n)?n.call(e):n},x.mixin=function(e){T(x.functions(e),function(t){var n=x[t]=e[t];x.prototype[t]=function(){var e=[this._wrapped];return o.apply(e,arguments),F.call(this,n.apply(x,e))}})};var P=0;x.uniqueId=function(e){var t=++P+"";return e?e+t:t},x.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var H=/(.)^/,B={"'":"'","\\":"\\","\r":"r","\n":"n"," ":"t","\u2028":"u2028","\u2029":"u2029"},j=/\\|'|\r|\n|\t|\u2028|\u2029/g;x.template=function(e,t,n){var r;n=x.defaults({},n,x.templateSettings);var i=new RegExp([(n.escape||H).source,(n.interpolate||H).source,(n.evaluate||H).source].join("|")+"|$","g"),s=0,o="__p+='";e.replace(i,function(t,n,r,i,u){return o+=e.slice(s,u).replace(j,function(e){return"\\"+B[e]}),n&&(o+="'+\n((__t=("+n+"))==null?'':_.escape(__t))+\n'"),r&&(o+="'+\n((__t=("+r+"))==null?'':__t)+\n'"),i&&(o+="';\n"+i+"\n__p+='"),s=u+t.length,t}),o+="';\n",n.variable||(o="with(obj||{}){\n"+o+"}\n"),o="var __t,__p='',__j=Array.prototype.join,print=function(){__p+=__j.call(arguments,'');};\n"+o+"return __p;\n";try{r=new Function(n.variable||"obj","_",o)}catch(u){throw u.source=o,u}if(t)return r(t,x);var a=function(e){return r.call(this,e,x)};return a.source="function("+(n.variable||"obj")+"){\n"+o+"}",a},x.chain=function(e){return x(e).chain()};var F=function(e){return this._chain?x(e).chain():e};x.mixin(x),T(["pop","push","reverse","shift","sort","splice","unshift"],function(e){var t=r[e];x.prototype[e]=function(){var n=this._wrapped;return t.apply(n,arguments),(e=="shift"||e=="splice")&&n.length===0&&delete n[0],F.call(this,n)}}),T(["concat","join","slice"],function(e){var t=r[e];x.prototype[e]=function(){return F.call(this,t.apply(this._wrapped,arguments))}}),x.extend(x.prototype,{chain:function(){return this._chain=!0,this},value:function(){return this._wrapped}})}.call(this),define("libs/underscore",function(e){return function(){var t,n;return t||e._}}(this)),define("utils/utils",["libs/underscore"],function(e){function t(e,t,r){n("GET",e,{},t,r)}function n(e,t,n,r,i){if(e=="GET"||e=="DELETE")t.indexOf("?")==-1?t+="?":t+="&",t+=$.param(n);var s=new XMLHttpRequest;s.open(e,t,!0),s.setRequestHeader("Accept","application/json"),s.setRequestHeader("Cache-Control","no-cache"),s.setRequestHeader("X-Requested-With","XMLHttpRequest"),s.setRequestHeader("Content-Type","application/json"),s.onloadend=function(){var e=s.status;try{response=jQuery.parseJSON(s.responseText)}catch(t){response=s.responseText}e==200?r&&r(response):i&&i(response)},e=="GET"||e=="DELETE"?s.send():s.send(JSON.stringify(n))}function r(e,t){var n=$('<div class="'+e+'"></div>');n.appendTo(":eq(0)");var r=n.css(t);return n.remove(),r}function i(e){$('link[href^="'+e+'"]').length||$('<link href="'+galaxy_config.root+e+'" rel="stylesheet">').appendTo("head")}function s(t,n){return t?e.defaults(t,n):n}function o(e,t){var n="";if(e>=1e11)e/=1e11,n="TB";else if(e>=1e8)e/=1e8,n="GB";else if(e>=1e5)e/=1e5,n="MB";else if(e>=100)e/=100,n="KB";else{if(!(e>0))return"<strong>-</strong>";e*=10,n="b"}var r=Math.round(e)/10;return t?r+" "+n:"<strong>"+r+"</strong> "+n}function u(){return(new Date).getTime().toString(36)}function a(e){var t=$("<p></p>");return t.append(e),t}function f(){var e=new Date,t=(e.getHours()<10?"0":"")+e.getHours(),n=(e.getMinutes()<10?"0":"")+e.getMinutes(),r=e.getDate()+"/"+(e.getMonth()+1)+"/"+e.getFullYear()+", "+t+":"+n;return r}return{cssLoadFile:i,cssGetAttribute:r,get:t,merge:s,bytesToString:o,uuid:u,time:f,wrap:a,request:n}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_histogram_discrete/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram (discrete)",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",columns:{y:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others"})}),define("plugin/charts/nvd3_line_focus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others"})}),define("plugin/charts/nvd3_pie/config",[],function(){return{title:"Pie chart",library:"nvd3.js",category:"Area charts",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bar/config","plugin/charts/nvd3_bar_stacked/config","plugin/charts/nvd3_bar_horizontal/config","plugin/charts/nvd3_bar_horizontal_stacked/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_histogram_discrete/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,highcharts_boxplot:p,heatmap:d}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/_nvd3/config.js
--- a/config/plugins/visualizations/charts/static/charts/_nvd3/config.js
+++ /dev/null
@@ -1,218 +0,0 @@
-define([], function() {
-
-return {
- title : '',
- columns : {
- y : {
- title : 'Values for y-axis'
- }
- },
- settings : {
- separator_label : {
- title : 'X axis',
- type : 'separator'
- },
- x_axis_label : {
- title : 'Axis label',
- info : 'Provide a label for the axis.',
- type : 'text',
- init : 'X-axis',
- placeholder : 'Axis label'
- },
- x_axis_type : {
- title : 'Axis value type',
- info : 'Select the value type of the axis.',
- type : 'select',
- init : 'auto',
- data : [
- {
- label : '-- Do not show values --',
- value : 'hide',
- hide : 'x_axis_tick'
- },
- {
- label : 'Auto',
- value : 'auto',
- hide : 'x_axis_tick'
- },
- {
- label : 'Float',
- value : 'f',
- show : 'x_axis_tick'
- },
- {
- label : 'Exponent',
- value : 'e',
- show : 'x_axis_tick'
- },
- {
- label : 'Integer',
- value : 'd',
- hide : 'x_axis_tick'
- },
- {
- label : 'Percentage',
- value : 'p',
- show : 'x_axis_tick'
- },
- {
- label : 'Rounded',
- value : 'r',
- show : 'x_axis_tick'
- },
- {
- label : 'SI-prefix',
- value : 's',
- show : 'x_axis_tick'
- }
- ]
- },
- x_axis_tick : {
- title : 'Axis tick format',
- info : 'Select the tick format for the axis.',
- type : 'select',
- init : '.1',
- data : [
- {
- label : '0.00001',
- value : '.5'
- },
- {
- label : '0.0001',
- value : '.4'
- },
- {
- label : '0.001',
- value : '.3'
- },
- {
- label : '0.01',
- value : '.2'
- },
- {
- label : '0.1',
- value : '.1'
- },
- {
- label : '1',
- value : '1'
- }
- ]
-
- },
- separator_tick : {
- title : 'Y axis',
- type : 'separator'
- },
- y_axis_label : {
- title : 'Axis label',
- info : 'Provide a label for the axis.',
- type : 'text',
- init : 'Y-axis',
- placeholder : 'Axis label'
- },
- y_axis_type : {
- title : 'Axis value type',
- info : 'Select the value type of the axis.',
- type : 'select',
- init : 'auto',
- data : [
- {
- label : '-- Do not show values --',
- value : 'hide',
- hide : 'y_axis_tick'
- },
- {
- label : 'Auto',
- value : 'auto',
- hide : 'y_axis_tick'
- },
- {
- label : 'Float',
- value : 'f',
- show : 'y_axis_tick'
- },
- {
- label : 'Exponent',
- value : 'e',
- show : 'y_axis_tick'
- },
- {
- label : 'Integer',
- value : 'd',
- hide : 'y_axis_tick'
- },
- {
- label : 'Percentage',
- value : 'p',
- show : 'y_axis_tick'
- },
- {
- label : 'Rounded',
- value : 'r',
- show : 'y_axis_tick'
- },
- {
- label : 'SI-prefix',
- value : 's',
- show : 'y_axis_tick'
- }
- ]
- },
- y_axis_tick : {
- title : 'Axis tick format',
- info : 'Select the tick format for the axis.',
- type : 'select',
- init : '.1',
- data : [
- {
- label : '0.00001',
- value : '.5'
- },
- {
- label : '0.0001',
- value : '.4'
- },
- {
- label : '0.001',
- value : '.3'
- },
- {
- label : '0.01',
- value : '.2'
- },
- {
- label : '0.1',
- value : '.1'
- },
- {
- label : '1',
- value : '1'
- }
- ]
-
- },
- separator_legend : {
- title : 'Others',
- type : 'separator'
- },
- show_legend : {
- title : 'Show legend',
- info : 'Would you like to add a legend?',
- type : 'select',
- init : 'true',
- data : [
- {
- label : 'Yes',
- value : 'true'
- },
- {
- label : 'No',
- value : 'false'
- }
- ]
- },
- }
-};
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
--- a/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
+++ /dev/null
@@ -1,80 +0,0 @@
-// dependencies
-define([], function() {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, nvd3_model, chart, request_dictionary, callback)
- {
- // request data
- var self = this;
- this.app.datasets.request(request_dictionary, function(data) {
- nv.addGraph(function() {
- // x axis
- self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick'));
-
- // x axis label
- nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label'));
-
- // y axis
- self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick'));
-
- // y axis label
- nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label'))
- .axisLabelDistance(30);
-
- // controls
- if (chart.groups.length == 1) {
- nvd3_model.options({ showControls: false });
- }
-
- // legend
- var legend_visible = true;
- if (chart.settings.get('show_legend') == 'false') {
- legend_visible = false;
- }
- nvd3_model.showLegend(legend_visible);
-
- // custom callback
- if (callback) {
- callback(nvd3_model);
- }
-
- // parse data to svg
- self.options.svg.datum(data)
- .call(nvd3_model);
-
- // refresh on window resize
- nv.utils.windowResize(nvd3_model.update);
-
- // set chart state
- chart.state('ok', 'Chart has been drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- });
- });
- },
-
- // make axis
- _axis: function(axis, type, tick) {
- switch (type) {
- case 'hide':
- axis.tickFormat(function() { return '' });
- break;
- case 'auto':
- break;
- default:
- axis.tickFormat(d3.format(tick + type));
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
--- a/config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/bardiagram/config.js
--- a/config/plugins/visualizations/charts/static/charts/bardiagram/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Bar diagram',
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/heatmap/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js
@@ -0,0 +1,195 @@
+define([], function() {
+
+return {
+ title : 'Heatmap',
+ category : 'Data processing (requires \'charts\' tool from Toolshed)',
+ library : '',
+ tag : 'div',
+ use_panels : true,
+ execute : 'heatmap',
+
+ // columns
+ columns : {
+ row_label : {
+ title : 'Row labels',
+ is_label : true
+ },
+ col_label : {
+ title : 'Column labels',
+ is_label : true
+ },
+ value : {
+ title : 'Observations'
+ },
+ },
+
+ // settings
+ settings: {
+ /*limit : {
+ title : 'Limit',
+ info : 'Which to ranked clusters would you like to visualize',
+ type : 'select',
+ init : '20',
+ data : [
+ {
+ label : '20',
+ value : '20'
+ },
+ {
+ label : '30',
+ value : '30'
+ },
+ {
+ label : '40',
+ value : '40'
+ },
+ {
+ label : '50',
+ value : '50'
+ },
+ {
+ label : '60',
+ value : '60'
+ },
+ {
+ label : '70',
+ value : '70'
+ },
+ {
+ label : '80',
+ value : '80'
+ },
+ {
+ label : '90',
+ value : '90'
+ },
+ {
+ label : '100',
+ value : '100'
+ }
+ ]
+ },*/
+ color_set : {
+ title : 'Color scheme',
+ info : 'Select a color scheme for your heatmap',
+ type : 'select',
+ init : 'ocean',
+ data : [
+ {
+ label : 'Cold-to-Hot',
+ value : 'hot'
+ },
+ {
+ label : 'Cool',
+ value : 'cool'
+ },
+ {
+ label : 'Copper',
+ value : 'copper'
+ },
+ {
+ label : 'Gebco',
+ value : 'gebco'
+ },
+ {
+ label : 'Globe',
+ value : 'globe'
+ },
+ {
+ label : 'Gray scale',
+ value : 'gray'
+ },
+ {
+ label : 'Haxby',
+ value : 'haxby'
+ },
+ {
+ label : 'Jet',
+ value : 'jet'
+ },
+ {
+ label : 'No-Green',
+ value : 'no_green'
+ },
+ {
+ label : 'Ocean',
+ value : 'ocean'
+ },
+ {
+ label : 'Polar',
+ value : 'polar'
+ },
+ {
+ label : 'Rainbow',
+ value : 'rainbow'
+ },
+ {
+ label : 'Red-to-Green',
+ value : 'redgreen'
+ },
+ {
+ label : 'Red-to-green (saturated)',
+ value : 'red2green'
+ },
+ {
+ label : 'Relief',
+ value : 'relief'
+ },
+ {
+ label : 'Seismograph',
+ value : 'seis'
+ },
+ {
+ label : 'Sealand',
+ value : 'sealand'
+ },
+ {
+ label : 'Split',
+ value : 'split'
+ },
+ {
+ label : 'Topo',
+ value : 'topo'
+ },
+ {
+ label : 'Wysiwyg',
+ value : 'wysiwyg'
+ }
+ ]
+ },
+
+ sorting : {
+ title : 'Sorting',
+ info : 'How should the columns be clustered?',
+ type : 'select',
+ init : 'hclust',
+ data : [
+ {
+ label : 'Read from dataset',
+ value : 'hclust'
+ },
+ {
+ label : 'Sort column and row labels',
+ value : 'byboth'
+ },
+ {
+ label : 'Sort column labels',
+ value : 'bycolumns'
+ },
+ {
+ label : 'Sort by rows',
+ value : 'byrow'
+ }
+ ]
+ }
+ },
+
+ // menu definition
+ menu : function() {
+ return {
+ color_set : this.settings.color_set
+ }
+ }
+};
+
+});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js
@@ -0,0 +1,52 @@
+// dependencies
+define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) {
+
+// color palettes
+var colorSets = {
+ seis: ['#AA0000', '#D00000', '#F70000', '#FF1D00', '#FF4400', '#FF6A00', '#FF9000', '#FFB700', '#FFDD00', '#FFFF00', '#FFFF00', '#FFFF00', '#BDFF0C', '#73FF1A', '#3FFA36', '#16F45A', '#00D08B', '#0087CD', '#0048FA', '#0024E3'],
+
+ sealand: ['#8C66FF', '#6A66FF', '#6684FF', '#66A7FF', '#66CAFF', '#66ECFF', '#66FFF0', '#66FFCE', '#66FFAB', '#66FF88', '#66FF66', '#88FF66', '#ABFF66', '#CEFF66', '#FFEEA6', '#FFD3A6', '#FFB8A6', '#FFAAB0', '#FFB5CB', '#FFC0E1'],
+
+ redgreen: ['#005824', '#1A693B', '#347B53', '#4F8D6B', '#699F83', '#83B09B', '#9EC2B3', '#B8D4CB', '#D2E6E3', '#EDF8FB', '#FFFFFF', '#F1EEF6', '#E6D3E1','#DBB9CD', '#D19EB9', '#C684A4', '#BB6990', '#B14F7C', '#A63467', '#9B1A53', '#91003F'],
+
+ ocean: ['#000000', '#000209', '#000413', '#00061E', '#000728', '#000932', '#002650', '#00426E', '#005E8C', '#007AAA', '#0096C8', '#22A9C2', '#45BCBB', '#67CFB5', '#8AE2AE', '#ACF6A8', '#BCF8B9', '#CBF9CA', '#DBFBDC', '#EBFDED'],
+
+ cool: ['#00FFFF', '#0DF2FF', '#19E6FF', '#26D9FF', '#33CCFF', '#3FBFFF', '#4CB3FF', '#59A6FF', '#6699FF', '#738CFF', '#7F7FFF', '#8C73FF', '#9966FF', '#A659FF', '#B24DFF', '#BF3FFF', '#CC33FF', '#D926FF', '#E619FF', '#F20DFF'],
+
+ copper: ['#000000', '#100906', '#1F130D', '#301E13', '#40281A', '#50321F', '#603C26', '#70462D', '#805033', '#905A3A', '#A06440', '#B06E46', '#C0784D', '#D08253', '#E08C5A', '#F09660', '#FFA066', '#FFAA6D', '#FFB473', '#FFBE7A'],
+
+ gebco: ['#00F0FF', '#00F0FF', '#00F0FF', '#23FFFF', '#23FFFF', '#23FFFF', '#5AFFFF', '#5AFFFF', '#5AFFFF', '#8CFFE6', '#8CFFE6', '#8CFFE6', '#A5FFD7', '#A5FFD7', '#A5FFD7', '#C3FFD7', '#C3FFD7', '#C3FFD7', '#D2FFD7', '#E6FFF0'],
+
+ globe: ['#9900FF', '#9900FF', '#7722FF', '#5544FF', '#3366FF', '#1188FF', '#1BA4FF', '#51BAFF', '#86D0FF', '#BCE6FF', '#336600', '#F3CA89', '#D9A627', '#A49019', '#9F7B0D', '#996600', '#B27676', '#C2B0B0', '#E5E5E5', '#FFFFFF'],
+
+ gray: ['#000000', '#0D0D0D', '#191919', '#262626', '#333333', '#3F3F3F', '#4C4C4C', '#595959', '#666666', '#737373', '#7F7F7F', '#8C8C8C', '#999999', '#A6A6A6', '#B2B2B2', '#BFBFBF', '#CCCCCC', '#D9D9D9', '#E6E6E6', '#F2F2F2'],
+
+ haxby: ['#090079', '#280096', '#0009C8', '#0019D4', '#1A66F0', '#19AFFF', '#32BEFF', '#61E1F0', '#6AECE1', '#8AECAE', '#CDFFA2', '#DFF68D', '#F8D768', '#FFBD57', '#F4754B', '#FF5A5A', '#FF7C7C', '#F6B3AE', '#FFC4C4', '#FFECEC'],
+
+ hot: ['#000000', '#220000', '#440000', '#660000', '#880000', '#AA0000', '#CC0000', '#EE0000', '#FF1100', '#FF3300', '#FF5500', '#FF7700', '#FF9900', '#FFBB00', '#FFDD00', '#FFFF00', '#FFFF33', '#FFFF66', '#FFFF99', '#FFFFCC'],
+
+ jet: ['#00007F', '#0000B2', '#0000E5', '#0019FF', '#004DFF', '#007FFF', '#00B2FF', '#00E5FF', '#FFFFF2', '#FFFFD9', '#FFFFBF', '#FFFFA5', '#FFFF8C', '#FFE500', '#FFB300', '#FF7F00', '#FF4C00', '#FF1900', '#E50000', '#B20000'],
+
+ no_green: ['#1F60FF', '#1F60FF', '#1F9FFF', '#1FBFFF', '#00CFFF', '#2AFFFF', '#2AFFFF', '#55FFFF', '#7FFFFF', '#AAFFFF', '#FFFF54', '#FFFF54', '#FFF000', '#FFBF00', '#FFA800', '#FF8A00', '#FF8A00', '#FF7000', '#FF4D00', '#FF0000'],
+
+ polar: ['#0000FF', '#1919FF', '#3333FF', '#4C4CFF', '#6666FF', '#7F7FFF', '#9999FF', '#B2B2FF', '#CCCCFF', '#E6E6FF', '#FFFFFF', '#FFE5E5', '#FFCCCC', '#FFB2B2', '#FF9999', '#FF7F7F', '#FF6666', '#FF4C4C', '#FF3333', '#FF1A1A'],
+
+ rainbow: ['#FF00FF', '#BF00FF', '#7F00FF', '#3F00FF', '#0000FF', '#003FFF', '#007FFF', '#00BFFF', '#00FFFF', '#00FFBF', '#00FF7F', '#00FF3F', '#00FF00', '#3FFF00', '#7FFF00', '#BFFF00', '#FFFF00', '#FFBF00', '#FF7F00', '#FF3F00'],
+
+ red2green: ['#FF0000', '#FF1919', '#FF3333', '#FF4C4C', '#FF6666', '#FF7F7F', '#FF9999', '#FFB2B2', '#FFCCCC', '#FFE6E6', '#FFFFFF', '#E5FFE5', '#CCFFCC', '#B2FFB2', '#99FF99', '#7FFF7F', '#66FF66', '#4CFF4C', '#33FF33', '#1AFF1A'],
+
+ relief: ['#000000', '#000413', '#000728', '#002650', '#005E8C', '#0096C8', '#45BCBB', '#8AE2AE', '#BCF8B9', '#DBFBDC', '#467832', '#887438', '#B19D48', '#DBC758', '#FAE769', '#FAEB7E', '#FCED93', '#FCF1A7', '#FCF6C1', '#FDFAE0'],
+
+ split: ['#7F7FFF', '#6666E6', '#4D4DCC', '#3333B3', '#1A1A99', '#00007F', '#000066', '#00004D', '#000033', '#00001A', '#000000', '#1A0000', '#330000', '#4D0000', '#660000', '#7F0000', '#991A1A', '#B33333', '#CC4D4D', '#E66666'],
+
+ topo: ['#C977D9', '#A18AE6', '#8AA2E6', '#8BD1E7', '#8AF3CF', '#85F38E', '#BDF385', '#EDE485', '#F0B086', '#DE9F8B', '#74A3B3', '#99CC70', '#DCD68E', '#EDDFAD', '#F7E8CA', '#FFF9F3', '#FFF9F6', '#FFFBF9', '#FFFCFA', '#FFFEFD'],
+
+ wysiwyg: ['#3F003F', '#3F003F', '#3F00BF', '#003FFF', '#00A0FF', '#3FBFFF', '#3FBFFF', '#40E0FF', '#3FFFBF', '#3FFF3F', '#7FFF3F', '#BFFF3F', '#BFFF3F', '#FFE040', '#FFE040', '#FF6040', '#FF1F40', '#FF60C0', '#FFA0FF', '#FFA0FF']
+}
+
+// return
+return {
+ colorSets: colorSets
+}
+
+});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
@@ -0,0 +1,739 @@
+// dependencies
+define(['utils/utils'],
+function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+ // number of columns and rows
+ colNumber: 0,
+ rowNumber: 0,
+
+ // indices
+ rowIndex: [],
+ colIndex: [],
+
+ // labels
+ rowLabel: [],
+ colLabel: [],
+
+ // cell size
+ cellSize: 0,
+
+ // font size
+ fontSize: 0,
+
+ // color buckets
+ nColors: 0,
+
+ // margins as cells
+ margin : {
+ top : 5,
+ right : 5,
+ bottom : 5,
+ left : 5
+ },
+
+ // default settings
+ optionsDefault: {
+ title : '',
+ pace : 1000,
+ },
+
+ // initialize
+ initialize: function(options) {
+ // link this
+ var self = this;
+
+ // load options
+ this.options = Utils.merge(options, this.optionsDefault)
+
+ // check requirements
+ if (!this.options.data || !this.options.div || !this.options.colors) {
+ console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data and/or colors) missing.');
+ return;
+ }
+
+ // link data
+ this.data = this.options.data;
+
+ // set element
+ this.setElement(this.options.div);
+
+ //
+ // data indexing
+ //
+
+ // labels (in alphabetical order)
+ this.rowLabel = [];
+ this.colLabel = [];
+
+ // index (order from original dataset)
+ this.rowIndex = [];
+ this.colIndex = [];
+
+ // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting)
+ this.colRank = {};
+ this.rowRank = {};
+
+ //
+ // identify and parse labels
+ //
+ for (var i in this.data) {
+ var cell = this.data[i];
+
+ // add label to index list
+ var col_label = cell.col_label;
+ if (this.colRank[col_label] === undefined) {
+ this.colRank[col_label] = true;
+ this.colLabel.push(col_label);
+ this.colIndex.push(col_label);
+ }
+ var row_label = cell.row_label;
+ if (this.rowRank[row_label] === undefined) {
+ this.rowRank[row_label] = true;
+ this.rowLabel.push(row_label);
+ this.rowIndex.push(row_label);
+ }
+ }
+
+ //
+ // sort labels and update rank dictionary
+ //
+
+ // set sizes
+ this.rowNumber = this.rowLabel.length
+ this.colNumber = this.colLabel.length
+
+ // sort labels alphabetical
+ this.rowLabel.sort();
+ this.colLabel.sort();
+
+ // generate sorted key list for rows
+ for (var i in this.rowLabel) {
+ var row_label = this.rowLabel[i];
+ var row = parseInt(i);
+ this.rowRank[row_label] = row;
+ }
+
+ // generate sorted key list for columns
+ for (var i in this.colLabel) {
+ var col_label = this.colLabel[i];
+ var col = parseInt(i);
+ this.colRank[col_label] = col;
+ }
+
+ //
+ // parse indexing from rank dictionary to cells
+ //
+
+ // min/max
+ this.max = undefined;
+ this.min = undefined
+
+ // add indices to data
+ for (var i in this.data) {
+ // get cell data
+ var cell = this.data[i];
+
+ // add rank
+ cell.col = this.colRank[cell.col_label];
+ cell.row = this.rowRank[cell.row_label];
+
+ // identify max/min values
+ if (this.min == undefined || this.min > cell.value) {
+ this.min = cell.value;
+ }
+ if (this.max == undefined || this.max < cell.value) {
+ this.max = cell.value;
+ }
+ }
+
+ //
+ // translate original create cluster from order in original data
+ //
+
+ // generate sorted key list for columns
+ for (var i in this.colIndex) {
+ this.colIndex[i] = this.colRank[this.colIndex[i]];
+ }
+ // generate sorted key list for columns
+ for (var i in this.rowIndex) {
+ this.rowIndex[i] = this.rowRank[this.rowIndex[i]];
+ }
+
+ // middle
+ this.mid = (this.max + this.min) / 2;
+
+ //
+ // set colors
+ //
+
+ // identify buckets
+ this.nColors = this.options.colors.length;
+
+ // color scale
+ this.colorScale = d3.scale.quantile()
+ .domain([this.min, this.mid, this.max])
+ .range(this.options.colors);
+
+ //
+ // add ui elements
+ //
+ // create tooltip
+ this.$tooltip = $(this._templateTooltip());
+ this.$el.append(this.$tooltip);
+
+ //
+ // finally draw the heatmap
+ //
+ this._build();
+
+ // catch window resize event
+ $(window).resize(function () {
+ self._build();
+ });
+ },
+
+ _build: function() {
+ // link this
+ var self = this;
+
+ // container (full draw area)
+ this.widthContainer = this.$el.width();
+ this.heightContainer = this.$el.height();
+
+ // get grid dimensions
+ this.width = this.widthContainer;
+ this.height = this.heightContainer;
+
+ // calculate cell size
+ this.cellSize = Math.min(((this.height) / (this.rowNumber + this.margin.top + this.margin.bottom)),
+ (this.width / (this.colNumber + this.margin.left + this.margin.right)));
+
+ // set font size
+ this.fontSize = Math.min(this.cellSize, 16);
+
+ // set width/height for plugin
+ this.width = this.cellSize * this.colNumber;
+ this.height = this.cellSize * this.rowNumber;
+
+ // get dimensions
+ var margin = this.options.margin;
+ var width = this.width;
+ var height = this.height;
+
+ // reset svg
+ if (this.svg !== undefined) {
+ this.$el.find('svg').remove();
+ }
+
+ // add main group and translate
+ this.svg = d3.select(this.$el[0]).append('svg')
+ .append('g')
+ .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' +
+ (this.heightContainer - height) / 2 + ')');
+
+ // reset sorting
+ this.rowSortOrder = false;
+ this.colSortOrder = false;
+
+ // build
+ this.d3RowLabels = this._buildRowLabels();
+ this.d3ColLabels = this._buildColLabels();
+ this.d3HeatMap = this._buildHeatMap();
+ this.d3Legend = this._buildLegend();
+ this.d3Title = this._buildTitle();
+ },
+
+ // build title
+ _buildTitle: function() {
+ // link this
+ var self = this;
+
+ // gather data
+ var height = this.height;
+ var width = this.width;
+ var cellSize = this.cellSize;
+ var fontSize = this.fontSize;
+ var title = this.options.title;
+
+ // add title
+ return this.svg.append('g')
+ .append('text')
+ .attr('x', width / 2)
+ .attr('y', height + 3 * cellSize + fontSize + 3)
+ .attr('text-anchor', 'middle')
+ .text(title);
+ },
+
+ // build legend
+ _buildLegend: function() {
+ // link this
+ var self = this;
+
+ // gather data
+ var cellSize = this.cellSize;
+ var fontSize = this.fontSize;
+ var height = this.height;
+ var legendCellWidth = this.width / this.nColors;
+
+ // create range labels
+ var dataRange = [];
+ for(var i = 0; i < this.nColors; i++) {
+ dataRange.push('');
+ }
+
+ // prepare indices
+ var dataRangeMin = 0;
+ var dataRangeMid = parseInt((dataRange.length - 1) / 2);
+ var dataRangeMax = dataRange.length - 1;
+
+ // add labels
+ dataRange[dataRangeMin] = this.min;
+ dataRange[dataRangeMid] = this.mid;
+ dataRange[dataRangeMax] = this.max;
+
+ // create legend
+ var legend = this.svg.selectAll('.legend')
+ .data(dataRange)
+ .enter().append('g')
+ .attr('class', 'legend');
+
+ // add boxes
+ legend.append('rect')
+ .attr('x', function(d, i) {
+ return legendCellWidth * i;
+ })
+ .attr('y', height + cellSize)
+ .attr('width', legendCellWidth)
+ .attr('height', cellSize)
+ .style('fill', function(d, i) {
+ return self.options.colors[i];
+ });
+
+ // add text
+ legend.append('text')
+ .attr('class', 'mono')
+ .text(function(d) {
+ return d;
+ })
+ .attr('width', legendCellWidth)
+ .attr('x', function(d, i) {
+ return legendCellWidth * i;
+ })
+ .attr('y', height + cellSize - 3)
+ .style('font-size', fontSize + 'px');
+
+ // return
+ return legend;
+ },
+
+ // build column labels
+ _buildColLabels: function() {
+ // link this
+ var self = this;
+
+ // gather data
+ var cellSize = this.cellSize;
+ var fontSize = this.fontSize;
+ var colIndex = this.colIndex;
+ var colLabel = this.colLabel;
+
+ // column labels
+ var colLabels = this.svg.append('g')
+ .selectAll('.colLabelg')
+ .data(colLabel)
+ .enter()
+ .append('text')
+ .text(function (d) {
+ return d;
+ })
+ .attr('x', 0)
+ .attr('y', function (d, i) {
+ return colIndex.indexOf(i) * cellSize;
+ })
+ .style('font-size', fontSize + 'px')
+ .style('text-anchor', 'left')
+ .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)')
+ .attr('class', function (d, i) {
+ return 'colLabel mono c' + i;
+ })
+ .on('mouseover', function(d) {
+ d3.select(this).classed('text-hover',true);
+ })
+ .on('mouseout' , function(d) {
+ d3.select(this).classed('text-hover',false);
+ })
+ .on('click', function(d, i) {
+ self.colSortOrder=!self.colSortOrder;
+ self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder);
+ d3.select('#order').property('selectedIndex', 4).node().focus();
+ });
+
+ // return
+ return colLabels;
+ },
+
+ // build row labels
+ _buildRowLabels: function() {
+ // link this
+ var self = this;
+
+ // gather data
+ var cellSize = this.cellSize;
+ var fontSize = this.fontSize;
+ var rowIndex = this.rowIndex;
+ var rowLabel = this.rowLabel;
+
+ // draw labels
+ var rowLabels = this.svg.append('g')
+ .selectAll('.rowLabelg')
+ .data(rowLabel)
+ .enter()
+ .append('text')
+ .text(function (d) {
+ return d;
+ })
+ .attr('x', 0)
+ .attr('y', function (d, i) {
+ return rowIndex.indexOf(i) * cellSize;
+ })
+ .style('font-size', fontSize + 'px')
+ .style('text-anchor', 'end')
+ .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')')
+ .attr('class', function (d, i) {
+ return 'rowLabel mono r' + i;
+ } )
+ .on('mouseover', function(d) {
+ d3.select(this).classed('text-hover',true);
+ })
+ .on('mouseout' , function(d) {
+ d3.select(this).classed('text-hover',false);
+ })
+ .on('click', function(d, i) {
+ self.rowSortOrder=!self.rowSortOrder;
+ self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder);
+ d3.select('#order').property('selectedIndex', 4).node().focus();
+ });
+
+ // return
+ return rowLabels;
+ },
+
+ // build heat map
+ _buildHeatMap: function() {
+ // link this
+ var self = this;
+
+ // gather data
+ var cellSize = this.cellSize;
+ var rowIndex = this.rowIndex;
+ var rowLabel = this.rowLabel;
+ var colIndex = this.colIndex;
+ var colLabel = this.colLabel;
+
+ // heat map
+ var heatmap = this.svg.append('g').attr('class','g3')
+ .selectAll('.cellg')
+ .data(self.data, function(d) {
+ return d.row + ':' + d.col;
+ })
+ .enter()
+ .append('rect')
+ .attr('x', function(d) {
+ return colIndex.indexOf(d.col) * cellSize;
+ })
+ .attr('y', function(d) {
+ return rowIndex.indexOf(d.row) * cellSize;
+ })
+ .attr('class', function(d){
+ return 'cell cell-border cr' + d.row + ' cc' + d.col;
+ })
+ .attr('width', cellSize)
+ .attr('height', cellSize)
+ .style('fill', function(d) {
+ return self.colorScale(d.value);
+ })
+ .on('mouseover', function(d){
+ // highlight text
+ d3.select(this).classed('cell-hover',true);
+ d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);});
+ d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);});
+
+ // update the tooltip position and value
+ d3.select('#heatmap-tooltip')
+ .style('left', (d3.event.pageX+10) + 'px')
+ .style('top', (d3.event.pageY-10) + 'px')
+ .select('#value')
+ .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value);
+ // show the tooltip
+ d3.select('#heatmap-tooltip').classed('hidden', false);
+ })
+ .on('mouseout', function(){
+ d3.select(this).classed('cell-hover',false);
+ d3.selectAll('.rowLabel').classed('text-highlight',false);
+ d3.selectAll('.colLabel').classed('text-highlight',false);
+ d3.select('#heatmap-tooltip').classed('hidden', true);
+ });
+
+ // return
+ return heatmap;
+ },
+
+ // change ordering of cells
+ _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) {
+ // get cell size
+ var cellSize = this.cellSize;
+
+ // define transition / prepare element
+ var t = this.svg.transition().duration(this.options.pace);
+
+ // create cells
+ var cells=[];
+ for (var i = 0; i < n; i++) {
+ cells[i] = {
+ value: this.min - 1
+ }
+ cells[i][rowORcol] = i;
+ }
+
+ // collect cells
+ t.selectAll('.c' + rORc + index).filter(function(ce) {
+ cells[ce[rowORcol]].value = ce.value;
+ });
+
+ // sort cells
+ cells.sort(function(a, b) {
+ if (sortOrder) {
+ return b.value - a.value;
+ } else {
+ return a.value - b.value;
+ }
+ });
+
+ // get sorted key list
+ var sorted = [];
+ for (var i in cells) {
+ sorted.push(cells[i][rowORcol]);
+ }
+
+ // rows or columns
+ if(rORc == 'r') {
+ // sort cells
+ t.selectAll('.cell')
+ .attr('x', function(d) {
+ return sorted.indexOf(d.col) * cellSize;
+ });
+
+ // sort labels
+ t.selectAll('.colLabel')
+ .attr('y', function (d, i) {
+ return sorted.indexOf(i) * cellSize;
+ });
+ } else {
+ // sort cells
+ t.selectAll('.cell')
+ .attr('y', function(d) {
+ return sorted.indexOf(d.row) * cellSize;
+ });
+
+ // sort labels
+ t.selectAll('.rowLabel')
+ .attr('y', function (d, i) {
+ return sorted.indexOf(i) * cellSize;
+ });
+ }
+ },
+
+ // sort function
+ _sortByOrder: function (value) {
+ // link this
+ var self = this;
+
+ // gather data
+ var cellSize = this.cellSize;
+ var rowIndex = this.rowIndex;
+ var rowLabel = this.rowLabel;
+ var colIndex = this.colIndex;
+ var colLabel = this.colLabel;
+
+ // set duration / select element
+ var t = this.svg.transition().duration(this.options.pace);
+ if(value=='hclust'){
+ t.selectAll('.cell')
+ .attr('x', function(d) {
+ return colIndex.indexOf(d.col) * cellSize;
+ })
+ .attr('y', function(d) {
+ return rowIndex.indexOf(d.row) * cellSize;
+ });
+
+ t.selectAll('.rowLabel')
+ .attr('y', function(d, i) {
+ return rowIndex.indexOf(i) * cellSize;
+ });
+
+ t.selectAll('.colLabel')
+ .attr('y', function(d, i) {
+ return colIndex.indexOf(i) * cellSize;
+ });
+
+ } else if (value=='byboth') {
+ t.selectAll('.cell')
+ .attr('x', function(d) {
+ return d.col * cellSize;
+ })
+ .attr('y', function(d) {
+ return d.row * cellSize;
+ });
+
+ t.selectAll('.rowLabel')
+ .attr('y', function (d, i) {
+ return i * cellSize;
+ });
+
+ t.selectAll('.colLabel')
+ .attr('y', function (d, i) {
+ return i * cellSize;
+ });
+ } else if (value=='byrow') {
+ t.selectAll('.cell')
+ .attr('y', function(d) {
+ return d.row * cellSize;
+ });
+
+ t.selectAll('.rowLabel')
+ .attr('y', function (d, i) {
+ return i * cellSize;
+ });
+ } else if (value=='bycol'){
+ t.selectAll('.cell')
+ .attr('x', function(d) {
+ return d.col * cellSize;
+ });
+ t.selectAll('.colLabel')
+ .attr('y', function (d, i) {
+ return i * cellSize;
+ });
+ }
+ },
+
+ // selection of cells
+ _addSelectionTool: function() {
+ //
+ // selection
+ //
+ var sa=d3.select('.g3')
+ .on('mousedown', function() {
+ if( !d3.event.altKey) {
+ d3.selectAll('.cell-selected').classed('cell-selected', false);
+ d3.selectAll('.rowLabel').classed('text-selected', false);
+ d3.selectAll('.colLabel').classed('text-selected', false);
+ }
+ var p = d3.mouse(this);
+ sa.append('rect')
+ .attr({
+ rx : 0,
+ ry : 0,
+ class : 'selection',
+ x : p[0],
+ y : p[1],
+ width : 1,
+ height : 1
+ })
+ })
+ .on('mousemove', function() {
+ var s = sa.select('rect.selection');
+
+ if(!s.empty()) {
+ var p = d3.mouse(this),
+ d = {
+ x : parseInt(s.attr('x'), 10),
+ y : parseInt(s.attr('y'), 10),
+ width : parseInt(s.attr('width'), 10),
+ height : parseInt(s.attr('height'), 10)
+ },
+ move = {
+ x : p[0] - d.x,
+ y : p[1] - d.y
+ };
+
+ if(move.x < 1 || (move.x*2<d.width)) {
+ d.x = p[0];
+ d.width -= move.x;
+ } else {
+ d.width = move.x;
+ }
+
+ if(move.y < 1 || (move.y*2<d.height)) {
+ d.y = p[1];
+ d.height -= move.y;
+ } else {
+ d.height = move.y;
+ }
+ s.attr(d);
+
+ // deselect all temporary selected state objects
+ d3.selectAll('.cell-selection.cell-selected').classed('cell-selected', false);
+ d3.selectAll('.text-selection.text-selected').classed('text-selected',false);
+ d3.selectAll('.cell').filter(function(cell_d, i) {
+ if(!d3.select(this).classed('cell-selected') &&
+ // inner circle inside selection frame
+ (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width &&
+ (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height)
+ {
+ d3.select(this)
+ .classed('cell-selection', true)
+ .classed('cell-selected', true);
+
+ d3.select('.r' + cell_d.row)
+ .classed('text-selection',true)
+ .classed('text-selected',true);
+
+ d3.select('.c' + cell_d.col)
+ .classed('text-selection',true)
+ .classed('text-selected',true);
+ }
+ });
+ }
+ })
+ .on('mouseup', function() {
+ // remove selection frame
+ sa.selectAll('rect.selection').remove();
+
+ // remove temporary selection marker class
+ d3.selectAll('.cell-selection').classed('cell-selection', false);
+ d3.selectAll('.text-selection').classed('text-selection', false);
+ })
+ .on('mouseout', function() {
+ if(d3.event.relatedTarget.tagName=='html') {
+ // remove selection frame
+ sa.selectAll('rect.selection').remove();
+
+ // remove temporary selection marker class
+ d3.selectAll('.cell-selection').classed('cell-selection', false);
+ d3.selectAll('.rowLabel').classed('text-selected',false);
+ d3.selectAll('.colLabel').classed('text-selected',false);
+ }
+ });
+ },
+
+ // template
+ _templateSelect: function() {
+ return '<select id="order">' +
+ '<option value="hclust">Cluster</option>' +
+ '<option value="byboth">Sort by row and column</option>' +
+ '<option value="byrow">Sort by row label</option>' +
+ '<option value="bycol">Sort by column label</option>' +
+ '</select>';
+ },
+
+ // template
+ _templateTooltip: function() {
+ return '<div id="heatmap-tooltip" class="hidden">' +
+ '<p><span id="value"></p>'
+ '</div>';
+ }
+});
+});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/heatmap/logo.png
Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js
@@ -0,0 +1,86 @@
+// dependencies
+define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'],
+function(Utils, HeatmapPlugin, HeatmapParameters) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // link this
+ var self = this;
+
+ // loop through data groups
+ var index = 0;
+ for (var group_index in request_dictionary.groups) {
+
+ // configure request
+ var tmp_dict = {
+ id : request_dictionary.id,
+ groups : [{
+ key : request_dictionary.groups[group_index].key,
+ columns : {
+ row_label: {
+ index : index++,
+ is_label : true
+ },
+ col_label: {
+ index : index++,
+ is_label : true
+ },
+ value: {
+ index : index++
+ }
+ }
+ }]
+ };
+
+ // target div
+ var group_div = self.options.canvas[group_index];
+
+ // draw group
+ this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) {
+ if (group_index == request_dictionary.groups.length - 1) {
+ // set chart state
+ chart.state('ok', 'Heat map drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ }
+ });
+ }
+ },
+
+ // draw group
+ _draw_group: function(group_index, div, chart, request_dictionary, callback) {
+ // link this
+ var self = this;
+
+ // request data
+ this.app.datasets.request(request_dictionary, function() {
+
+ // get group
+ var group = request_dictionary.groups[0];
+
+ // draw plot
+ var heatmap = new HeatmapPlugin({
+ 'title' : group.key,
+ 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')],
+ 'data' : group.values,
+ 'div' : div
+ });
+
+ // callback on completion
+ callback (group_index);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
@@ -0,0 +1,40 @@
+define([], function() {
+
+return {
+ title : 'Box plot',
+ category : 'Data processing (requires \'charts\' tool from Toolshed)',
+ library : 'highcharts.js',
+ tag : 'div',
+ execute : 'boxplot',
+ columns : {
+ y : {
+ title : 'Observations'
+ }
+ },
+ settings : {
+ separator_label : {
+ title : 'X axis',
+ type : 'separator'
+ },
+ x_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'X-axis',
+ placeholder : 'Axis label'
+ },
+ separator_tick : {
+ title : 'Y axis',
+ type : 'separator'
+ },
+ y_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'Y-axis',
+ placeholder : 'Axis label'
+ }
+ }
+};
+
+});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png
Binary file config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png has changed
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js
@@ -0,0 +1,122 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+ // highcharts configuration
+ hc_config : {
+ chart: {
+ type: 'boxplot'
+ },
+
+ title: {
+ text: ''
+ },
+
+ legend: {
+ enabled: false
+ },
+
+ credits: {
+ enabled: false
+ },
+
+ plotOptions: {
+ series: {
+ animation: false
+ }
+ },
+
+ xAxis: {
+ categories: [],
+ title: {
+ text: ''
+ }
+ },
+
+ yAxis: {
+ title: {
+ text: ''
+ }
+ },
+
+ series: [{
+ name: 'Details:',
+ data: [],
+ tooltip: {
+ headerFormat: '<em>{point.key}</em><br/>'
+ }
+ }]
+ },
+
+ // initialize
+ initialize: function(app, options) {
+ this.app = app;
+ this.options = options;
+ },
+
+ // render
+ draw : function(process_id, chart, request_dictionary)
+ {
+ // configure request
+ var index = 0;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = null;
+ group.columns = {
+ x: {
+ index: index++
+ }
+ }
+ }
+
+ // set axis labels
+ this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label');
+ this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label');
+
+ // request data
+ var self = this;
+ this.app.datasets.request(request_dictionary, function() {
+
+ // reset data/categories
+ var data = [];
+ var categories = [];
+
+ // loop through data groups
+ for (var key in request_dictionary.groups) {
+ // get group
+ var group = request_dictionary.groups[key];
+
+ // add category
+ categories.push(group.key);
+
+ // format chart data
+ var point = [];
+ for (var key in group.values) {
+ point.push(group.values[key].x);
+ }
+
+ // add to data
+ data.push (point);
+ }
+
+ // categories
+ self.hc_config.xAxis.categories = categories;
+
+ // update data
+ self.hc_config.series[0].data = data;
+
+ // draw plot
+ self.options.canvas[0].highcharts(self.hc_config);
+
+ // set chart state
+ chart.state('ok', 'Box plot drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/histogram/config.js
--- a/config/plugins/visualizations/charts/static/charts/histogram/config.js
+++ /dev/null
@@ -1,21 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Histogram',
- execute : true,
- columns : {
- y : {
- title : 'Observations'
- }
- },
- settings : {
- x_axis_label : {
- init : 'Breaks'
- },
- y_axis_label : {
- init : 'Density'
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/histogram/histogram.js
--- a/config/plugins/visualizations/charts/static/charts/histogram/histogram.js
+++ /dev/null
@@ -1,31 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // configure request
- var index = 0;
- for (var i in request_dictionary.groups) {
- var group = request_dictionary.groups[i];
- group.columns = {
- x: index++,
- y: index++
- }
- }
-
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/horizontal/config.js
--- a/config/plugins/visualizations/charts/static/charts/horizontal/config.js
+++ /dev/null
@@ -1,12 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Bar diagram (horizontal)',
- settings : {
- x_axis_type : {
- init : 'hide'
- }
- }
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
--- a/config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/line/config.js
--- a/config/plugins/visualizations/charts/static/charts/line/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Line chart',
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/line/line.js
--- a/config/plugins/visualizations/charts/static/charts/line/line.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
--- a/config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
+++ /dev/null
@@ -1,7 +0,0 @@
-define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
- title : 'Line with focus',
-});
-
-});
\ No newline at end of file
diff -r 8c4e3b85aa3bdf896a826e50acb2714b6b45279c -r 9ebe5ccabe0259801c67138ddf7f1734b011d694 config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
--- a/config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
+++ /dev/null
@@ -1,21 +0,0 @@
-// dependencies
-define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- var nvd3 = new NVD3(this.app, this.options);
- nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary);
- }
-});
-
-});
\ No newline at end of file
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
commit/galaxy-central: dan: Fix for tool shed handling new GenomeBuilds manager.
by commits-noreply＠bitbucket.org 19 May '14
by commits-noreply＠bitbucket.org 19 May '14
19 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9b33b543fb14/
Changeset: 9b33b543fb14
User: dan
Date: 2014-05-19 21:35:58
Summary: Fix for tool shed handling new GenomeBuilds manager.
Affected #: 2 files
diff -r 3faf01e5111ecf454f06b22546b530131b0550be -r 9b33b543fb1448f8f775ac975e2605ac610c8f63 lib/galaxy/webapps/tool_shed/app.py
--- a/lib/galaxy/webapps/tool_shed/app.py
+++ b/lib/galaxy/webapps/tool_shed/app.py
@@ -6,6 +6,7 @@
import galaxy.datatypes.registry
import galaxy.webapps.tool_shed.model
from galaxy.openid.providers import OpenIDProviders
+from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web import security
from galaxy.tags.tag_handler import CommunityTagHandler
from tool_shed.grids.util import RepositoryGridFilterManager
@@ -49,6 +50,7 @@
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path )
+ self.genome_builds = GenomeBuilds( self )
# The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
self.toolbox = tools.ToolBox( [], self.config.tool_path, self )
# Initialize the Tool Shed security agent.
diff -r 3faf01e5111ecf454f06b22546b530131b0550be -r 9b33b543fb1448f8f775ac975e2605ac610c8f63 lib/galaxy/webapps/tool_shed/config.py
--- a/lib/galaxy/webapps/tool_shed/config.py
+++ b/lib/galaxy/webapps/tool_shed/config.py
@@ -53,6 +53,7 @@
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() )
self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
+ self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root )
self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None )
# Install and test framework for testing tools contained in repositories.
self.num_tool_test_results_saved = kwargs.get( 'num_tool_test_results_saved', 5 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
commit/galaxy-central: dan: First pass at allowing dbkeys / genome builds to be loaded from Tool Data Tables.
by commits-noreply＠bitbucket.org 19 May '14
by commits-noreply＠bitbucket.org 19 May '14
19 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3faf01e5111e/
Changeset: 3faf01e5111e
User: dan
Date: 2014-05-19 21:08:26
Summary: First pass at allowing dbkeys / genome builds to be loaded from Tool Data Tables.
Affected #: 12 files
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -57,13 +57,17 @@
self.tag_handler = GalaxyTagHandler()
# Dataset Collection Plugins
self.dataset_collections_service = dataset_collections.DatasetCollectionsService(self)
+
+ # Tool Data Tables
+ self._configure_tool_data_tables( from_shed_config=False )
+ # Load dbkey / genome build manager
+ self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True )
+
# Genomes
self.genomes = Genomes( self )
# Data providers registry.
self.data_provider_registry = DataProviderRegistry()
- self._configure_tool_data_tables( from_shed_config=False )
-
# Initialize job metrics manager, needs to be in place before
# config so per-destination modifications can be made.
self.job_metrics = job_metrics.JobMetrics( self.config.job_metrics_config_file, app=self )
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -16,6 +16,7 @@
from galaxy.util import string_as_bool
from galaxy.util import listify
from galaxy.util import parse_xml
+from galaxy.util.dbkeys import GenomeBuilds
from galaxy import eggs
import pkg_resources
@@ -554,6 +555,9 @@
""" Shared code for configuring Galaxy-like app objects.
"""
+ def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ):
+ self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style )
+
def _configure_toolbox( self ):
# Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
tool_configs = self.config.tool_configs
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -372,7 +372,7 @@
context = context or {}
other_values = other_values or {}
try:
- values = kwd['trans'].db_builds
+ values = kwd['trans'].app.genome_builds.get_genome_build_names( kwd['trans'] )
except KeyError:
pass
return super(DBKeyParameter, self).get_html_field( value, context, other_values, values, **kwd)
@@ -381,7 +381,7 @@
context = context or {}
other_values = other_values or {}
try:
- values = kwd['trans'].db_builds
+ values = kwd['trans'].app.genome_builds.get_genome_build_names( kwd['trans'] )
except KeyError:
pass
return super(DBKeyParameter, self).get_html( value, context, other_values, values, **kwd)
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -193,36 +193,10 @@
# Collect chromInfo dataset and add as parameters to incoming
db_datasets = {}
- db_dataset = trans.db_dataset_for( input_dbkey )
+ ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans )
if db_dataset:
- db_datasets[ "chromInfo" ] = db_dataset
- incoming[ "chromInfo" ] = db_dataset.file_name
- else:
- # -- Get chrom_info (len file) from either a custom or built-in build. --
-
- chrom_info = None
- if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
- # Custom build.
- custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
- # HACK: the attempt to get chrom_info below will trigger the
- # fasta-to-len converter if the dataset is not available or,
- # which will in turn create a recursive loop when
- # running the fasta-to-len tool. So, use a hack in the second
- # condition below to avoid getting chrom_info when running the
- # fasta-to-len converter.
- if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len':
- # Build is defined by fasta; get len file, which is obtained from converting fasta.
- build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
- chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
- elif 'len' in custom_build_dict:
- # Build is defined by len file, so use it.
- chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
-
- if not chrom_info:
- # Default to built-in build.
- chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey )
- incoming[ "chromInfo" ] = os.path.abspath( chrom_info )
- inp_data.update( db_datasets )
+ inp_data.update( { "chromInfo": db_dataset } )
+ incoming[ "chromInfo" ] = chrom_info
# Determine output dataset permission/roles list
existing_datasets = [ inp for inp in inp_data.values() if inp ]
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/tools/actions/upload_common.py
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -157,7 +157,7 @@
folder = matches[0]
else:
new_folder = trans.app.model.LibraryFolder( name=name, description='Automatically created by upload tool' )
- new_folder.genome_build = util.dbnames.default_value
+ new_folder.genome_build = trans.app.genome_builds.default_value
folder.add_folder( new_folder )
trans.sa_session.add( new_folder )
trans.sa_session.flush()
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -321,6 +321,19 @@
def get_fields( self ):
return self.data
+ def get_named_fields_list( self ):
+ rval = []
+ named_colums = self.get_column_name_list()
+ for fields in self.get_fields():
+ field_dict = {}
+ for i, field in enumerate( fields ):
+ field_name = named_colums[i]
+ if field_name is None:
+ field_name = i #check that this is supposed to be 0 based.
+ field_dict[ field_name ] = field
+ rval.append( field_dict )
+ return rval
+
def get_version_fields( self ):
return ( self._loaded_content_version, self.data )
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1033,17 +1033,18 @@
"""
def __init__( self, *args, **kwds ):
super( GenomeBuildParameter, self ).__init__( *args, **kwds )
- self.static_options = [ ( value, key, False ) for key, value in util.dbnames ]
+ if self.tool:
+ self.static_options = [ ( value, key, False ) for key, value in self._get_dbkey_names()]
def get_options( self, trans, other_values ):
last_used_build = object()
if trans.history:
last_used_build = trans.history.genome_build
- for dbkey, build_name in trans.db_builds:
+ for dbkey, build_name in self._get_dbkey_names( trans=trans ):
yield build_name, dbkey, ( dbkey == last_used_build )
def get_legal_values( self, trans, other_values ):
- return set( dbkey for dbkey, _ in trans.db_builds )
+ return set( dbkey for dbkey, _ in self._get_dbkey_names( trans=trans ) )
def to_dict( self, trans, view='collection', value_mapper=None ):
# skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
@@ -1062,6 +1063,12 @@
'value': value
})
return d
+
+ def _get_dbkey_names( self, trans=None ):
+ if not self.tool:
+ # Hack for unit tests, since we have no tool
+ return util.dbnames
+ return self.tool.app.genome_builds.get_genome_build_names( trans=trans )
class ColumnListParameter( SelectToolParameter ):
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/util/dbkeys.py
--- /dev/null
+++ b/lib/galaxy/util/dbkeys.py
@@ -0,0 +1,82 @@
+"""
+Functionality for dealing with dbkeys.
+"""
+#dbkeys read from disk using builds.txt
+from galaxy.util import dbnames, galaxy_directory
+from galaxy.util.json import from_json_string
+from galaxy.util.odict import odict
+import os.path
+
+
+class GenomeBuilds( object ):
+ default_value = "?"
+ default_name = "unspecified (?)"
+
+ def __init__( self, app, data_table_name="__dbkeys__", load_old_style=True ):
+ self._app = app
+ self._data_table_name = data_table_name
+ self._static_chrom_info_path = app.config.len_file_path
+ self._static_dbkeys = odict() #need odict to keep ? at top of list
+ if load_old_style:
+ for key, value in dbnames:
+ self._static_dbkeys[ key ] = value
+
+ def get_genome_build_names( self, trans=None ):
+ #FIXME: how to deal with key duplicates?
+ #Load old builds.txt static keys
+ rval = ( self._static_dbkeys.items() )
+ #load dbkeys from dbkey data table
+ dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None )
+ if dbkey_table is not None:
+ for field_dict in dbkey_table.get_named_fields_list():
+ rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) )
+ #load user custom genome builds
+ if trans is not None:
+ if trans.history:
+ datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \
+ .filter_by( deleted=False, history_id=trans.history.id, extension="len" )
+ for dataset in datasets:
+ rval.append( (dataset.dbkey, dataset.name) )
+ user = trans.get_user()
+ if user and 'dbkeys' in user.preferences:
+ user_keys = from_json_string( user.preferences['dbkeys'] )
+ for key, chrom_dict in user_keys.iteritems():
+ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) )
+ return rval
+
+ def get_chrom_info( self, dbkey, trans=None ):
+ chrom_info = None
+ db_dataset = None
+ # Collect chromInfo from custom builds
+ if trans:
+ db_dataset = trans.db_dataset_for( dbkey )
+ if db_dataset:
+ #incoming[ "chromInfo" ] = db_dataset.file_name
+ chrom_info = db_dataset.file_name
+ else:
+ # -- Get chrom_info (len file) from either a custom or built-in build. --
+ if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
+ # Custom build.
+ custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
+ # HACK: the attempt to get chrom_info below will trigger the
+ # fasta-to-len converter if the dataset is not available or,
+ # which will in turn create a recursive loop when
+ # running the fasta-to-len tool. So, use a hack in the second
+ # condition below to avoid getting chrom_info when running the
+ # fasta-to-len converter.
+ if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len':
+ # Build is defined by fasta; get len file, which is obtained from converting fasta.
+ build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
+ chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
+ elif 'len' in custom_build_dict:
+ # Build is defined by len file, so use it.
+ chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
+ if not chrom_info:
+ dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None )
+ if dbkey_table is not None:
+ chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None )
+ if not chrom_info:
+ # Default to built-in build.
+ chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey )
+ chrom_info = os.path.abspath( chrom_info )
+ return ( chrom_info, db_dataset )
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/visualization/genomes.py
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -178,9 +178,9 @@
"""
def __init__( self, app ):
- # Create list of genomes from util.dbnames
+ # Create list of genomes from app.genome_builds
self.genomes = {}
- for key, description in util.dbnames:
+ for key, description in app.genome_builds.get_genome_build_names():
self.genomes[ key ] = Genome( key, description )
# Add len files to genomes.
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -1075,7 +1075,7 @@
if self.galaxy_session.user:
history.user = self.galaxy_session.user
# Track genome_build with history
- history.genome_build = util.dbnames.default_value
+ history.genome_build = self.app.genome_builds.default_value
# Set the user's default history permissions
self.app.security_agent.history_set_default_permissions( history )
# Save
@@ -1238,19 +1238,8 @@
Returns the builds defined by galaxy and the builds defined by
the user (chromInfo in history).
"""
- dbnames = list()
- if self.history:
- datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \
- .filter_by( deleted=False, history_id=self.history.id, extension="len" )
- for dataset in datasets:
- dbnames.append( (dataset.dbkey, dataset.name) )
- user = self.get_user()
- if user and 'dbkeys' in user.preferences:
- user_keys = from_json_string( user.preferences['dbkeys'] )
- for key, chrom_dict in user_keys.iteritems():
- dbnames.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key) ))
- dbnames.extend( util.dbnames )
- return dbnames
+ #FIXME: This method should be removed
+ return self.app.genome_builds.get_genome_build_names( trans=self )
@property
def ucsc_builds( self ):
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be lib/galaxy/webapps/galaxy/controllers/library_common.py
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -292,9 +292,9 @@
new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ),
description=util.restore_text( params.description ) )
# We are associating the last used genome build with folders, so we will always
- # initialize a new folder with the first dbkey in util.dbnames which is currently
+ # initialize a new folder with the first dbkey in genome builds list which is currently
# ? unspecified (?)
- new_folder.genome_build = util.dbnames.default_value
+ new_folder.genome_build = trans.app.genome_builds.default_value
parent_folder.add_folder( new_folder )
trans.sa_session.add( new_folder )
trans.sa_session.flush()
@@ -1433,7 +1433,7 @@
file_formats = trans.app.datatypes_registry.upload_file_formats
# Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
def get_dbkey_options( last_used_build ):
- for dbkey, build_name in util.dbnames:
+ for dbkey, build_name in trans.app.genome_builds.get_genome_build_names( trans=trans ):
yield build_name, dbkey, ( dbkey==last_used_build )
dbkeys = get_dbkey_options( last_used_build )
# Send the current history to the form to enable importing datasets from history to library
diff -r 6e4db406d614c7826b80a825be351df674994409 -r 3faf01e5111ecf454f06b22546b530131b0550be test/unit/tools_support.py
--- a/test/unit/tools_support.py
+++ b/test/unit/tools_support.py
@@ -14,6 +14,7 @@
from galaxy.model import mapping
from galaxy.tools import Tool
from galaxy.util import parse_xml
+from galaxy.util.dbkeys import GenomeBuilds
from galaxy.jobs import NoopQueue
@@ -96,6 +97,7 @@
tool_data_path=os.path.join(test_directory, "tools"),
root=os.path.join(test_directory, "galaxy"),
admin_users="mary(a)example.com",
+ len_file_path=os.path.join( 'tool-data', 'shared', 'ucsc', 'chrom' ),
)
# Setup some attributes for downstream extension by specific tests.
@@ -115,6 +117,7 @@
self.model[ module_member_name ] = module_member
else:
self.model = in_memomry_model
+ self.genome_builds = GenomeBuilds( self )
self.toolbox = None
self.object_store = None
self.security = SecurityHelper(id_secret="testing")
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/50e08b9c5329/
Changeset: 50e08b9c5329
User: jmchilton
Date: 2014-05-19 20:36:49
Summary: Don't show different multi-run option button if only one option.
Affected #: 1 file
diff -r 175bacc005a1437bfeedc8c76fe757467c08a870 -r 50e08b9c53293f52cbfe2c7e3e5dc9326e7c442f static/scripts/galaxy.tools.js
--- a/static/scripts/galaxy.tools.js
+++ b/static/scripts/galaxy.tools.js
@@ -68,6 +68,7 @@
var view = this;
var index = 0;
+ var visibleCount = 0;
_.each( this.switchOptions, function( option, onValue ) {
var numValues = _.size( option.options );
var selectionType = SELECTION_TYPE[ onValue ];
@@ -79,15 +80,21 @@
hidden = true;
}
if( ! hidden ) {
- var button = $('<i class="fa ' + selectionType['icon_class'] + '" style="padding-left: 5px; padding-right: 2px;"></i>').click(function() {
+ visibleCount++;
+ var button = $('<i class="fa ' + selectionType['icon_class'] + ' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function() {
view.enableSelectBy( iIndex, onValue );
}).attr(
'title',
selectionType['select_by']
);
- view.formRow().find( "label" ).append( button );
+ view.formRow().find( "label" ).append( button );
}
});
+ if( visibleCount < 2 ) {
+ // Don't show buttons to switch options...
+ view.formRow().find("i.runOptionIcon").hide();
+ }
+
if( defaultIndex != null) {
view.enableSelectBy( defaultIndex, defaultOption );
}
https://bitbucket.org/galaxy/galaxy-central/commits/6e4db406d614/
Changeset: 6e4db406d614
User: jmchilton
Date: 2014-05-19 20:38:21
Summary: Pack scripts.
Affected #: 1 file
diff -r 50e08b9c53293f52cbfe2c7e3e5dc9326e7c442f -r 6e4db406d614c7826b80a825be351df674994409 static/scripts/packed/galaxy.tools.js
--- a/static/scripts/packed/galaxy.tools.js
+++ b/static/scripts/packed/galaxy.tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/tools"],function(c,b){var a=function(g,f){$("input[name='"+g+"'][type='checkbox']").attr("checked",!!f)};$("div.checkUncheckAllPlaceholder").each(function(){var f=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){a(f,true)});unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){a(f,false)});$(this).append(select_link).append(" ").append(unselect_link)});var e={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:true},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:false,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:false},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:true},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:false,},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:true},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:false,}};var d=Backbone.View.extend({initialize:function(k){var g=k.default_option;var l=null;var j=k.switch_options;this.switchOptions=j;this.prefix=k.prefix;var i=this.$el;var f=this;var h=0;c.each(this.switchOptions,function(q,s){var m=c.size(q.options);var p=e[s];var o=h++;var r=false;if(g==s){l=o}else{if(m<(p.min_option_count||1)){r=true}}if(!r){var n=$('<i class="fa '+p.icon_class+'" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){f.enableSelectBy(o,s)}).attr("title",p.select_by);f.formRow().find("label").append(n)}});if(l!=null){f.enableSelectBy(l,g)}},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(k,j){var h=e[j];if(h.allow_remap){$("div#remap-row").css("display","none")}else{$("div#remap-row").css("display","inherit")}this.formRow().find("i").each(function(l,m){if(l==k){$(m).css("color","black")}else{$(m).css("color","Gray")}});var g=this.$("select");var f=this.switchOptions[j];g.attr("name",this.prefix+f.name);g.attr("multiple",f.multiple);var i=this.$(".select2-container").length>0;g.html("");c.each(f.options,function(m){var o=m[0];var n=m[1];var l=m[2];g.append($("<option />",{text:o,val:n,selected:l}))});if(i){g.select2()}}});return{SwitchSelectView:d}});
\ No newline at end of file
+define(["libs/underscore","mvc/tools"],function(c,b){var a=function(g,f){$("input[name='"+g+"'][type='checkbox']").attr("checked",!!f)};$("div.checkUncheckAllPlaceholder").each(function(){var f=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){a(f,true)});unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){a(f,false)});$(this).append(select_link).append(" ").append(unselect_link)});var e={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:true},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:false,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:false},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:true},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:false,},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:true},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:false,}};var d=Backbone.View.extend({initialize:function(l){var g=l.default_option;var m=null;var k=l.switch_options;this.switchOptions=k;this.prefix=l.prefix;var j=this.$el;var f=this;var h=0;var i=0;c.each(this.switchOptions,function(r,t){var n=c.size(r.options);var q=e[t];var p=h++;var s=false;if(g==t){m=p}else{if(n<(q.min_option_count||1)){s=true}}if(!s){i++;var o=$('<i class="fa '+q.icon_class+' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){f.enableSelectBy(p,t)}).attr("title",q.select_by);f.formRow().find("label").append(o)}});if(i<2){f.formRow().find("i.runOptionIcon").hide()}if(m!=null){f.enableSelectBy(m,g)}},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(k,j){var h=e[j];if(h.allow_remap){$("div#remap-row").css("display","none")}else{$("div#remap-row").css("display","inherit")}this.formRow().find("i").each(function(l,m){if(l==k){$(m).css("color","black")}else{$(m).css("color","Gray")}});var g=this.$("select");var f=this.switchOptions[j];g.attr("name",this.prefix+f.name);g.attr("multiple",f.multiple);var i=this.$(".select2-container").length>0;g.html("");c.each(f.options,function(m){var o=m[0];var n=m[1];var l=m[2];g.append($("<option />",{text:o,val:n,selected:l}))});if(i){g.select2()}}});return{SwitchSelectView:d}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c559805d44df/
Changeset: c559805d44df
User: davebgx
Date: 2014-05-19 19:01:46
Summary: Migrate 22 tools from the distribution to the tool shed.
Affected #: 67 files
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
--- /dev/null
+++ b/lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
@@ -0,0 +1,62 @@
+"""
+The following tools have been eliminated from the distribution:
+
+1: Profile Annotations for a set of genomic intervals
+2: Polymorphism of the Reads
+3: Coverage of the Reads in wiggle format
+4: Canonical Correlation Analysis
+5: Convert Color Space to Nucleotides
+6: Compute sequence length
+7: Concatenate FASTA alignment by species
+8: Filter sequences by length
+9: FASTA-to-Tabular converter
+10: FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data
+11: Kernel Canonical Correlation Analysis
+12: Kernel Principal Component Analysis
+13: Format mapping data as UCSC custom track
+14: Megablast compare short reads against htgs, nt, and wgs databases
+15: Parse blast XML output
+16: Principal Component Analysis
+17: RMAP for Solexa Short Reads Alignment
+18: RMAPQ for Solexa Short Reads Alignment with Quality Scores
+19: Histogram of high quality score reads
+20: Build base quality distribution
+21: Select high quality segments
+22: Tabular-to-FASTA
+
+The tools are now available in the repositories respectively:
+
+1: annotation_profiler
+2: blat_coverage_report
+3: blat_mapping
+4: canonical_correlation_analysis
+5: convert_solid_color2nuc
+6: fasta_compute_length
+7: fasta_concatenate_by_species
+8: fasta_filter_by_length
+9: fasta_to_tabular
+10: fastqsolexa_to_fasta_qual
+11: kernel_canonical_correlation_analysis
+12: kernel_principal_component_analysis
+13: mapping_to_ucsc
+14: megablast_wrapper
+15: megablast_xml_parser
+16: principal_component_analysis
+17: rmap
+18: rmapq
+19: short_reads_figure_high_quality_length
+20: short_reads_figure_score
+21: short_reads_trim_seq
+22: tabular_to_fasta
+
+from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu
+and will be installed into your local Galaxy instance at the
+location discussed above by running the following command.
+
+"""
+
+def upgrade( migrate_engine ):
+ print __doc__
+
+def downgrade( migrate_engine ):
+ pass
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 scripts/migrate_tools/0011_tools.sh
--- /dev/null
+++ b/scripts/migrate_tools/0011_tools.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+cd `dirname $0`/../..
+python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml $@
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 scripts/migrate_tools/0011_tools.xml
--- /dev/null
+++ b/scripts/migrate_tools/0011_tools.xml
@@ -0,0 +1,69 @@
+<?xml version="1.0"?>
+<toolshed name="toolshed.g2.bx.psu.edu">
+ <repository changeset_revision="3b33da018e74" owner="devteam" name="annotation_profiler" description="Profile Annotations for a set of genomic intervals">
+ <tool file="annotation_profiler/annotation_profiler.xml" id="Annotation_Profiler_0" version="1.0.0" />
+ </repository>
+ <repository changeset_revision="30f0948c649c" owner="devteam" name="blat_coverage_report" description="Polymorphism of the Reads">
+ <tool id="generate_coverage_report" version="1.0.0" file="metag_tools/blat_coverage_report.xml" />
+ </repository>
+ <repository changeset_revision="807e3e50845a" owner="devteam" name="blat_mapping" description="Coverage of the Reads in wiggle format">
+ <tool id="blat2wig" version="1.0.0" file="metag_tools/blat_mapping.xml" />
+ </repository>
+ <repository changeset_revision="9bc0c48a027f" owner="devteam" name="canonical_correlation_analysis" description="Canonical Correlation Analysis">
+ <tool file="multivariate_stats/cca.xml" id="cca1" version="1.0.0" />
+ </repository>
+ <repository changeset_revision="ab28e7de2db3" owner="devteam" name="convert_solid_color2nuc" description="Convert Color Space to Nucleotides">
+ <tool id="color2nuc" version="1.0.0" file="metag_tools/convert_SOLiD_color2nuc.xm" />
+ </repository>
+ <repository changeset_revision="ece409f6573c" owner="devteam" name="fasta_compute_length" description="Compute sequence length">
+ <tool file="fasta_tools/fasta_compute_length.xml" id="fasta_compute_length" version="__VERSION__" />
+ </repository>
+ <repository changeset_revision="2126e1b833a2" owner="devteam" name="fasta_concatenate_by_species" description="Concatenate FASTA alignment by species">
+ <tool file="fasta_tools/fasta_concatenate_by_species.xml" id="fasta_concatenate0" version="0.0.0" />
+ </repository>
+ <repository changeset_revision="16679a7f554a" owner="devteam" name="fasta_filter_by_length" description="Filter sequences by length">
+ <tool file="fasta_tools/fasta_filter_by_length.xml" id="fasta_filter_by_length" version="1.1" />
+ </repository>
+ <repository changeset_revision="9d189d08f2ad" owner="devteam" name="fasta_to_tabular" description="FASTA-to-Tabular converter">
+ <tool file="fasta_tools/fasta_to_tabular.xml" id="fasta2tab" version="1.1.0" />
+ </repository>
+ <repository changeset_revision="ef23c03d7497" owner="devteam" name="fastqsolexa_to_fasta_qual" description="FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data">
+ <tool id="fastqsolexa_to_fasta_qual" version="1.0.0" file="metag_tools/fastqsolexa_to_fasta_qual.xml" />
+ </repository>
+ <repository changeset_revision="7a092113eb8c" owner="devteam" name="kernel_canonical_correlation_analysis" description="Kernel Canonical Correlation Analysis">
+ <tool file="multivariate_stats/kcca.xml" id="kcca1" version="1.0.0" />
+ </repository>
+ <repository changeset_revision="e9ebd4bfbdfc" owner="devteam" name="kernel_principal_component_analysis" description="Kernel Principal Component Analysis">
+ <tool file="multivariate_stats/kpca.xml" id="kpca1" version="1.0.0" />
+ </repository>
+ <repository changeset_revision="601abbd22cea" owner="devteam" name="mapping_to_ucsc" description="Format mapping data as UCSC custom track">
+ <tool id="mapToUCSC" version="1.0.0" file="metag_tools/mapping_to_ucsc.xml" />
+ </repository>
+ <repository changeset_revision="dc7b4acb3fa6" owner="devteam" name="megablast_wrapper" description="Megablast compare short reads against htgs, nt, and wgs databases">
+ <tool file="metag_tools/megablast_wrapper.xml" id="megablast_wrapper" version="1.2.0" />
+ </repository>
+ <repository changeset_revision="03ca082aeb2e" owner="devteam" name="megablast_xml_parser" description="Parse blast XML output">
+ <tool file="metag_tools/megablast_xml_parser.xml" id="megablast_xml_parser" version="1.0.0" />
+ </repository>
+ <repository changeset_revision="f568051cdf2e" owner="devteam" name="principal_component_analysis" description="Principal Component Analysis">
+ <tool file="multivariate_stats/pca.xml" id="pca1" version="1.0.2" />
+ </repository>
+ <repository changeset_revision="ee49255302d8" owner="devteam" name="rmap" description="RMAP for Solexa Short Reads Alignment">
+ <tool id="rmap_wrapper" version="1.0.0" file="metag_tools/rmap_wrapper.xml" />
+ </repository>
+ <repository changeset_revision="f6e5bb5aa2f5" owner="devteam" name="rmapq" description="RMAPQ for Solexa Short Reads Alignment with Quality Scores">
+ <tool id="rmapq_wrapper" version="1.0.0" file="metag_tools/rmapq_wrapper.xml" />
+ </repository>
+ <repository changeset_revision="556ceed24699" owner="devteam" name="short_reads_figure_high_quality_length" description="Histogram of high quality score reads">
+ <tool id="hist_high_quality_score" version="1.0.0" file="metag_tools/short_reads_figure_high_quality_length.xml" />
+ </repository>
+ <repository changeset_revision="b52b9c7aabd9" owner="devteam" name="short_reads_figure_score" description="Build base quality distribution">
+ <tool file="metag_tools/short_reads_figure_score.xml" id="quality_score_distribution" version="1.0.2" />
+ </repository>
+ <repository changeset_revision="f17a1585733b" owner="devteam" name="short_reads_trim_seq" description="Select high quality segments">
+ <tool file="metag_tools/short_reads_trim_seq.xml" id="trim_reads" version="1.0.0" />
+ </repository>
+ <repository changeset_revision="0b4e36026794" owner="devteam" name="tabular_to_fasta" description="Tabular-to-FASTA">
+ <tool file="fasta_tools/tabular_to_fasta.xml" id="tab2fasta" version="1.1.0" />
+ </repository>
+</toolshed>
\ No newline at end of file
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 scripts/tools/annotation_profiler/README.txt
--- a/scripts/tools/annotation_profiler/README.txt
+++ /dev/null
@@ -1,54 +0,0 @@
-This file explains how to create annotation indexes for the annotation profiler tool. Annotation profiler indexes are an exceedingly simple binary format,
-containing no header information and consisting of an ordered linear list of (start,stop encoded individually as '<I') regions which are covered by a UCSC table partitioned
-by chromosome name. Genomic regions are merged by overlap / direct adjacency (e.g. a table having ranges of: 1-10, 6-12, 12-20 and 25-28 results in two merged ranges of: 1-20 and 25-28).
-
-Files are arranged like:
-/profiled_annotations/DBKEY/TABLE_NAME/
- CHROMOSOME_NAME.covered
- CHROMOSOME_NAME.total_coverage
- CHROMOSOME_NAME.total_regions
-/profiled_annotations/DBKEY/
- DBKEY_tables.xml
- chromosomes.txt
- profiled_info.txt
-
-
-where CHROMOSOME_NAME.covered is the binary file, CHROMOSOME_NAME.total_coverage is a text file containing the integer count of bases covered by the
-table and CHROMOSOME_NAME.total_regions contains the integer count of the number of regions found in CHROMOSOME_NAME.covered
-
-DBKEY_tables.xml should be appended to the annotation profile available table configuration file (tool-data/annotation_profiler_options.xml).
-The DBKEY should also be added as a new line to the annotation profiler valid builds file (annotation_profiler_valid_builds.txt).
-The output (/profiled_annotations/DBKEY) should be made available as GALAXY_ROOT/tool-data/annotation_profiler/DBKEY.
-
-profiled_info.txt contains info on the generated annotations, separated by lines with tab-delimited label,value pairs:
- profiler_version - the version of the build_profile_indexes.py script that was used to generate the profiled data
- dbkey - the dbkey used for the run
- chromosomes - contains the names and lengths of chromosomes that were used to parse single-chromosome tables (tables divided into individual files by chromosome)
- dump_time - the declared dump time of the database, taken from trackDb.txt.gz
- profiled_time - seconds since epoch in utc for when the database dump was profiled
- database_hash - a md5 hex digest of all the profiled table info
-
-
-Typical usage includes:
-
-python build_profile_indexes.py -d hg19 -i /ucsc_data/hg19/database/ > hg19.txt
-
-where the genome build is hg19 and /ucsc_data/hg19/database/ contains the downloaded database dump from UCSC (e.g. obtained by rsync: rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ /ucsc_data/hg19/database/).
-
-
-
-By default, chromosome names come from a file named 'chromInfo.txt.gz' found in the input directory, with FTP used as a backup.
-When FTP is used to obtain the names of chromosomes from UCSC for a particular genome build, alternate ftp sites and paths can be specified by using the --ftp_site and --ftp_path attributes.
-Chromosome names can instead be provided on the commandline via the --chromosomes option, which accepts a comma separated list of:ChromName1[=length],ChromName2[=length],...
-
-
-
- usage = "usage: %prog options"
- parser = OptionParser( usage=usage )
- parser.add_option( '-d', '--dbkey', dest='dbkey', default='hg18', help='dbkey to process' )
- parser.add_option( '-i', '--input_dir', dest='input_dir', default=os.path.join( 'golden_path','%s', 'database' ), help='Input Directory' )
- parser.add_option( '-o', '--output_dir', dest='output_dir', default=os.path.join( 'profiled_annotations','%s' ), help='Output Directory' )
- parser.add_option( '-c', '--chromosomes', dest='chromosomes', default='', help='Comma separated list of: ChromName1[=length],ChromName2[=length],...' )
- parser.add_option( '-b', '--bitset_size', dest='bitset_size', default=DEFAULT_BITSET_SIZE, type='int', help='Default BitSet size; overridden by sizes specified in chromInfo.txt.gz or by --chromosomes' )
- parser.add_option( '-f', '--ftp_site', dest='ftp_site', default='hgdownload.cse.ucsc.edu', help='FTP site; used for chromosome info when chromInfo.txt.gz method fails' )
- parser.add_option( '-p', '--ftp_path', dest='ftp_path', default='/goldenPath/%s/chromosomes/', help='FTP Path; used for chromosome info when chromInfo.txt.gz method fails' )
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 scripts/tools/annotation_profiler/build_profile_indexes.py
--- a/scripts/tools/annotation_profiler/build_profile_indexes.py
+++ /dev/null
@@ -1,338 +0,0 @@
-#!/usr/bin/env python
-#Dan Blankenberg
-
-VERSION = '1.0.0' # version of this script
-
-from optparse import OptionParser
-import os, gzip, struct, time
-from ftplib import FTP #do we want a diff method than using FTP to determine Chrom Names, eg use local copy
-
-#import md5 from hashlib; if python2.4 or less, use old md5
-try:
- from hashlib import md5
-except ImportError:
- from md5 import new as md5
-
-#import BitSet from bx-python, try using eggs and package resources, fall back to any local installation
-try:
- from galaxy import eggs
- import pkg_resources
- pkg_resources.require( "bx-python" )
-except: pass #Maybe there is a local installation available
-from bx.bitset import BitSet
-
-#Define constants
-STRUCT_FMT = '<I'
-STRUCT_SIZE = struct.calcsize( STRUCT_FMT )
-DEFAULT_BITSET_SIZE = 300000000
-CHUNK_SIZE = 1024
-
-#Headers used to parse .sql files to determine column indexes for chromosome name, start and end
-alias_spec = {
- 'chromCol' : [ 'chrom' , 'CHROMOSOME' , 'CHROM', 'Chromosome Name', 'tName' ],
- 'startCol' : [ 'start' , 'START', 'chromStart', 'txStart', 'Start Position (bp)', 'tStart', 'genoStart' ],
- 'endCol' : [ 'end' , 'END' , 'STOP', 'chromEnd', 'txEnd', 'End Position (bp)', 'tEnd', 'genoEnd' ],
-}
-
-#Headers used to parse trackDb.txt.gz
-#TODO: these should be parsed directly from trackDb.sql
-trackDb_headers = ["tableName", "shortLabel", "type", "longLabel", "visibility", "priority", "colorR", "colorG", "colorB", "altColorR", "altColorG", "altColorB", "useScore", "private", "restrictCount", "restrictList", "url", "html", "grp", "canPack", "settings"]
-
-def get_columns( filename ):
- input_sql = open( filename ).read()
- input_sql = input_sql.split( 'CREATE TABLE ' )[1].split( ';' )[0]
- input_sql = input_sql.split( ' (', 1 )
- table_name = input_sql[0].strip().strip( '`' )
- input_sql = [ split.strip().split( ' ' )[0].strip().strip( '`' ) for split in input_sql[1].rsplit( ')', 1 )[0].strip().split( '\n' ) ]
- print input_sql
- chrom_col = None
- start_col = None
- end_col = None
- for col_name in alias_spec['chromCol']:
- for i, header_name in enumerate( input_sql ):
- if col_name == header_name:
- chrom_col = i
- break
- if chrom_col is not None:
- break
-
- for col_name in alias_spec['startCol']:
- for i, header_name in enumerate( input_sql ):
- if col_name == header_name:
- start_col = i
- break
- if start_col is not None:
- break
-
- for col_name in alias_spec['endCol']:
- for i, header_name in enumerate( input_sql ):
- if col_name == header_name:
- end_col = i
- break
- if end_col is not None:
- break
-
- return table_name, chrom_col, start_col, end_col
-
-
-def create_grouping_xml( input_dir, output_dir, dbkey ):
- output_filename = os.path.join( output_dir, '%s_tables.xml' % dbkey )
- def load_groups( file_name = 'grp.txt.gz' ):
- groups = {}
- for line in gzip.open( os.path.join( input_dir, file_name ) ):
- fields = line.split( '\t' )
- groups[fields[0]] = { 'desc': fields[1], 'priority': fields[2] }
- return groups
- f = gzip.open( os.path.join( input_dir, 'trackDb.txt.gz' ) )
- out = open( output_filename, 'wb' )
- tables = {}
- cur_buf = ''
- while True:
- line = f.readline()
- if not line: break
- #remove new lines
- line = line.rstrip( '\n\r' )
- line = line.replace( '\\\t', ' ' ) #replace escaped tabs with space
- cur_buf += "%s\n" % line.rstrip( '\\' )
- if line.endswith( '\\' ):
- continue #line is wrapped, next line
- #all fields should be loaded now...
- fields = cur_buf.split( '\t' )
- cur_buf = '' #reset buffer
- assert len( fields ) == len( trackDb_headers ), 'Failed Parsing trackDb.txt.gz; fields: %s' % fields
- table_name = fields[ 0 ]
- tables[ table_name ] = {}
- for field_name, field_value in zip( trackDb_headers, fields ):
- tables[ table_name ][ field_name ] = field_value
- #split settings fields into dict
- fields = fields[-1].split( '\n' )
- tables[ table_name ][ 'settings' ] = {}
- for field in fields:
- setting_fields = field.split( ' ', 1 )
- setting_name = setting_value = setting_fields[ 0 ]
- if len( setting_fields ) > 1:
- setting_value = setting_fields[ 1 ]
- if setting_name or setting_value:
- tables[ table_name ][ 'settings' ][ setting_name ] = setting_value
- #Load Groups
- groups = load_groups()
- in_groups = {}
- for table_name, values in tables.iteritems():
- if os.path.exists( os.path.join( output_dir, table_name ) ):
- group = values['grp']
- if group not in in_groups:
- in_groups[group]={}
- #***NAME CHANGE***, 'subTrack' no longer exists as a setting...use 'parent' instead
- #subTrack = values.get('settings', {} ).get( 'subTrack', table_name )
- subTrack = values.get('settings', {} ).get( 'parent', table_name ).split( ' ' )[0] #need to split, because could be e.g. 'trackgroup on'
- if subTrack not in in_groups[group]:
- in_groups[group][subTrack]=[]
- in_groups[group][subTrack].append( table_name )
-
- assigned_tables = []
- out.write( """<filter type="data_meta" data_ref="input1" meta_key="dbkey" value="%s">\n""" % ( dbkey ) )
- out.write( " <options>\n" )
- for group, subTracks in sorted( in_groups.iteritems() ):
- out.write( """ <option name="%s" value="group-%s">\n""" % ( groups[group]['desc'], group ) )
- for sub_name, sub_tracks in subTracks.iteritems():
- if len( sub_tracks ) > 1:
- out.write( """ <option name="%s" value="subtracks-%s">\n""" % ( sub_name, sub_name ) )
- sub_tracks.sort()
- for track in sub_tracks:
- track_label = track
- if "$" not in tables[track]['shortLabel']:
- track_label = tables[track]['shortLabel']
- out.write( """ <option name="%s" value="%s"/>\n""" % ( track_label, track ) )
- assigned_tables.append( track )
- out.write( " </option>\n" )
- else:
- track = sub_tracks[0]
- track_label = track
- if "$" not in tables[track]['shortLabel']:
- track_label = tables[track]['shortLabel']
- out.write( """ <option name="%s" value="%s"/>\n""" % ( track_label, track ) )
- assigned_tables.append( track )
- out.write( " </option>\n" )
- unassigned_tables = list( sorted( [ table_dir for table_dir in os.listdir( output_dir ) if table_dir not in assigned_tables and os.path.isdir( os.path.join( output_dir, table_dir ) ) ] ) )
- if unassigned_tables:
- out.write( """ <option name="Uncategorized Tables" value="group-trackDbUnassigned">\n""" )
- for table_name in unassigned_tables:
- out.write( """ <option name="%s" value="%s"/>\n""" % ( table_name, table_name ) )
- out.write( " </option>\n" )
- out.write( " </options>\n" )
- out.write( """</filter>\n""" )
- out.close()
-
-def write_database_dump_info( input_dir, output_dir, dbkey, chrom_lengths, default_bitset_size ):
- #generate hash for profiled table directories
- #sort directories off output root (files in output root not hashed, including the profiler_info.txt file)
- #sort files in each directory and hash file contents
- profiled_hash = md5()
- for table_dir in sorted( [ table_dir for table_dir in os.listdir( output_dir ) if os.path.isdir( os.path.join( output_dir, table_dir ) ) ] ):
- for filename in sorted( os.listdir( os.path.join( output_dir, table_dir ) ) ):
- f = open( os.path.join( output_dir, table_dir, filename ), 'rb' )
- while True:
- hash_chunk = f.read( CHUNK_SIZE )
- if not hash_chunk:
- break
- profiled_hash.update( hash_chunk )
- profiled_hash = profiled_hash.hexdigest()
-
- #generate hash for input dir
- #sort directories off input root
- #sort files in each directory and hash file contents
- database_hash = md5()
- for dirpath, dirnames, filenames in sorted( os.walk( input_dir ) ):
- for filename in sorted( filenames ):
- f = open( os.path.join( input_dir, dirpath, filename ), 'rb' )
- while True:
- hash_chunk = f.read( CHUNK_SIZE )
- if not hash_chunk:
- break
- database_hash.update( hash_chunk )
- database_hash = database_hash.hexdigest()
-
- #write out info file
- out = open( os.path.join( output_dir, 'profiler_info.txt' ), 'wb' )
- out.write( 'dbkey\t%s\n' % ( dbkey ) )
- out.write( 'chromosomes\t%s\n' % ( ','.join( [ '%s=%s' % ( chrom_name, chrom_len ) for chrom_name, chrom_len in chrom_lengths.iteritems() ] ) ) )
- out.write( 'bitset_size\t%s\n' % ( default_bitset_size ) )
- for line in open( os.path.join( input_dir, 'trackDb.sql' ) ):
- line = line.strip()
- if line.startswith( '-- Dump completed on ' ):
- line = line[ len( '-- Dump completed on ' ): ]
- out.write( 'dump_time\t%s\n' % ( line ) )
- break
- out.write( 'dump_hash\t%s\n' % ( database_hash ) )
- out.write( 'profiler_time\t%s\n' % ( time.time() ) )
- out.write( 'profiler_hash\t%s\n' % ( profiled_hash ) )
- out.write( 'profiler_version\t%s\n' % ( VERSION ) )
- out.write( 'profiler_struct_format\t%s\n' % ( STRUCT_FMT ) )
- out.write( 'profiler_struct_size\t%s\n' % ( STRUCT_SIZE ) )
- out.close()
-
-def __main__():
- usage = "usage: %prog options"
- parser = OptionParser( usage=usage )
- parser.add_option( '-d', '--dbkey', dest='dbkey', default='hg18', help='dbkey to process' )
- parser.add_option( '-i', '--input_dir', dest='input_dir', default=os.path.join( 'golden_path','%s', 'database' ), help='Input Directory' )
- parser.add_option( '-o', '--output_dir', dest='output_dir', default=os.path.join( 'profiled_annotations','%s' ), help='Output Directory' )
- parser.add_option( '-c', '--chromosomes', dest='chromosomes', default='', help='Comma separated list of: ChromName1[=length],ChromName2[=length],...' )
- parser.add_option( '-b', '--bitset_size', dest='bitset_size', default=DEFAULT_BITSET_SIZE, type='int', help='Default BitSet size; overridden by sizes specified in chromInfo.txt.gz or by --chromosomes' )
- parser.add_option( '-f', '--ftp_site', dest='ftp_site', default='hgdownload.cse.ucsc.edu', help='FTP site; used for chromosome info when chromInfo.txt.gz method fails' )
- parser.add_option( '-p', '--ftp_path', dest='ftp_path', default='/goldenPath/%s/chromosomes/', help='FTP Path; used for chromosome info when chromInfo.txt.gz method fails' )
-
- ( options, args ) = parser.parse_args()
-
- input_dir = options.input_dir
- if '%' in input_dir:
- input_dir = input_dir % options.dbkey
- assert os.path.exists( input_dir ), 'Input directory does not exist'
- output_dir = options.output_dir
- if '%' in output_dir:
- output_dir = output_dir % options.dbkey
- assert not os.path.exists( output_dir ), 'Output directory already exists'
- os.makedirs( output_dir )
- ftp_path = options.ftp_path
- if '%' in ftp_path:
- ftp_path = ftp_path % options.dbkey
-
- #Get chromosome names and lengths
- chrom_lengths = {}
- if options.chromosomes:
- for chrom in options.chromosomes.split( ',' ):
- fields = chrom.split( '=' )
- chrom = fields[0]
- if len( fields ) > 1:
- chrom_len = int( fields[1] )
- else:
- chrom_len = options.bitset_size
- chrom_lengths[ chrom ] = chrom_len
- chroms = chrom_lengths.keys()
- print 'Chrom info taken from command line option.'
- else:
- try:
- for line in gzip.open( os.path.join( input_dir, 'chromInfo.txt.gz' ) ):
- fields = line.strip().split( '\t' )
- chrom_lengths[ fields[0] ] = int( fields[ 1 ] )
- chroms = chrom_lengths.keys()
- print 'Chrom info taken from chromInfo.txt.gz.'
- except Exception, e:
- print 'Error loading chrom info from chromInfo.txt.gz, trying FTP method.'
- chrom_lengths = {} #zero out chrom_lengths
- chroms = []
- ftp = FTP( options.ftp_site )
- ftp.login()
- for name in ftp.nlst( ftp_path ):
- if name.endswith( '.fa.gz' ):
- chroms.append( name.split( '/' )[-1][ :-len( '.fa.gz' ) ] )
- ftp.close()
- for chrom in chroms:
- chrom_lengths[ chrom ] = options.bitset_size
- #sort chroms by length of name, decending; necessary for when table names start with chrom name
- chroms = list( reversed( [ chrom for chrom_len, chrom in sorted( [ ( len( chrom ), chrom ) for chrom in chroms ] ) ] ) )
-
- #parse tables from local files
- #loop through directory contents, if file ends in '.sql', process table
- for filename in os.listdir( input_dir ):
- if filename.endswith ( '.sql' ):
- base_filename = filename[ 0:-len( '.sql' ) ]
- table_out_dir = os.path.join( output_dir, base_filename )
- #some tables are chromosome specific, lets strip off the chrom name
- for chrom in chroms:
- if base_filename.startswith( "%s_" % chrom ):
- #found chromosome
- table_out_dir = os.path.join( output_dir, base_filename[len( "%s_" % chrom ):] )
- break
- #create table dir
- if not os.path.exists( table_out_dir ):
- os.mkdir( table_out_dir ) #table dir may already exist in the case of single chrom tables
- print "Created table dir (%s)." % table_out_dir
- else:
- print "Table dir (%s) already exists." % table_out_dir
- #find column assignments
- table_name, chrom_col, start_col, end_col = get_columns( "%s.sql" % os.path.join( input_dir, base_filename ) )
- if chrom_col is None or start_col is None or end_col is None:
- print "Table %s (%s) does not appear to have a chromosome, a start, or a stop." % ( table_name, "%s.sql" % os.path.join( input_dir, base_filename ) )
- if not os.listdir( table_out_dir ):
- print "Removing empty table (%s) directory (%s)." % ( table_name, table_out_dir )
- os.rmdir( table_out_dir )
- continue
- #build bitsets from table
- bitset_dict = {}
- for line in gzip.open( '%s.txt.gz' % os.path.join( input_dir, base_filename ) ):
- fields = line.strip().split( '\t' )
- chrom = fields[ chrom_col ]
- start = int( fields[ start_col ] )
- end = int( fields[ end_col ] )
- if chrom not in bitset_dict:
- bitset_dict[ chrom ] = BitSet( chrom_lengths.get( chrom, options.bitset_size ) )
- bitset_dict[ chrom ].set_range( start, end - start )
- #write bitsets as profiled annotations
- for chrom_name, chrom_bits in bitset_dict.iteritems():
- out = open( os.path.join( table_out_dir, '%s.covered' % chrom_name ), 'wb' )
- end = 0
- total_regions = 0
- total_coverage = 0
- max_size = chrom_lengths.get( chrom_name, options.bitset_size )
- while True:
- start = chrom_bits.next_set( end )
- if start >= max_size:
- break
- end = chrom_bits.next_clear( start )
- out.write( struct.pack( STRUCT_FMT, start ) )
- out.write( struct.pack( STRUCT_FMT, end ) )
- total_regions += 1
- total_coverage += end - start
- if end >= max_size:
- break
- out.close()
- open( os.path.join( table_out_dir, '%s.total_regions' % chrom_name ), 'wb' ).write( str( total_regions ) )
- open( os.path.join( table_out_dir, '%s.total_coverage' % chrom_name ), 'wb' ).write( str( total_coverage ) )
-
- #create xml
- create_grouping_xml( input_dir, output_dir, options.dbkey )
- #create database dump info file, for database version control
- write_database_dump_info( input_dir, output_dir, options.dbkey, chrom_lengths, options.bitset_size )
-
-if __name__ == "__main__": __main__()
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 static/images/blat_mapping_example.png
Binary file static/images/blat_mapping_example.png has changed
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 static/images/dualcolorcode.png
Binary file static/images/dualcolorcode.png has changed
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 static/images/short_reads_boxplot.png
Binary file static/images/short_reads_boxplot.png has changed
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 test-data/annotation_profiler_1.out
--- a/test-data/annotation_profiler_1.out
+++ /dev/null
@@ -1,9 +0,0 @@
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + multiz17way 1700000 1
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + mrna 1476531 12
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + multiz28way 1700000 1
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + refGene 1247808 15
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + knownAlt 14617 57
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + affyGnf1h 16218 2
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + snp126 8224 7262
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + acembly 1532618 20
-chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + knownGene 1282789 18
diff -r 1fae433a54eaaab6392da9e9a8eec94a3b568c14 -r c559805d44df064f98dfbc94b59edba7be01adb9 test-data/annotation_profiler_2.out
--- a/test-data/annotation_profiler_2.out
+++ /dev/null
@@ -1,10 +0,0 @@
-#tableName tableChromosomeCoverage tableChromosomeCount tableRegionCoverage tableRegionCount allIntervalCount allIntervalSize allCoverage allTableRegionsOverlaped allIntervalsOverlapingTable nrIntervalCount nrIntervalSize nrCoverage nrTableRegionsOverlaped nrIntervalsOverlapingTable
-multiz17way 1232617592 115 107496500 7 25 2178864 2178864 25 25 24 2178828 2178828 7 24
-mrna 610115393 8453 53577685 617 25 2178864 1904380 38 24 24 2178828 1904344 33 23
-multiz28way 1233785185 143 107466479 10 25 2178864 2178864 25 25 24 2178828 2178828 8 24
-refGene 496767116 7324 46112187 488 25 2178864 1677947 30 23 24 2178828 1677911 27 22
-knownAlt 8647368 20213 766619 1630 25 2178864 5612 31 11 24 2178828 5612 31 11
-affyGnf1h 24034558 3995 2446754 307 25 2178864 191851 9 6 24 2178828 191851 9 6
-snp126 5297125 4456213 382226 331523 25 2178864 9205 7074 25 24 2178828 9205 7074 24
-acembly 710938193 13800 63146381 938 25 2178864 1903560 35 24 24 2178828 1903524 30 23
-knownGene 555770538 7921 50317496 558 25 2178864 1822985 30 23 24 2178828 1822949 27 22
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/175bacc005a1/
Changeset: 175bacc005a1
User: davebgx
Date: 2014-05-19 19:02:11
Summary: Remove migrated tools from the tool conf files.
Affected #: 2 files
diff -r c559805d44df064f98dfbc94b59edba7be01adb9 -r 175bacc005a1437bfeedc8c76fe757467c08a870 tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -51,13 +51,6 @@
<tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" /></section>
- <section id="fasta_manipulation" name="FASTA manipulation">
- <tool file="fasta_tools/fasta_compute_length.xml" />
- <tool file="fasta_tools/fasta_filter_by_length.xml" />
- <tool file="fasta_tools/fasta_concatenate_by_species.xml" />
- <tool file="fasta_tools/fasta_to_tabular.xml" />
- <tool file="fasta_tools/tabular_to_fasta.xml" />
- </section><section id="filter" name="Filter and Sort"><tool file="stats/filtering.xml" /><tool file="filters/sorter.xml" />
@@ -97,9 +90,6 @@
<tool file="filters/wiggle_to_simple.xml" /><tool file="stats/aggregate_binned_scores_in_intervals.xml" /></section>
- <section id="bxops" name="Operate on Genomic Intervals">
- <tool file="annotation_profiler/annotation_profiler.xml" />
- </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" />
@@ -116,12 +106,6 @@
<tool file="maf/vcf_to_maf_customtrack.xml" /><tool file="mutation/visualize.xml" /></section>
- <section id="multVar" name="Multivariate Analysis">
- <tool file="multivariate_stats/pca.xml" />
- <tool file="multivariate_stats/cca.xml" />
- <tool file="multivariate_stats/kpca.xml" />
- <tool file="multivariate_stats/kcca.xml" />
- </section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" />
@@ -141,8 +125,6 @@
<section id="cshl_library_information" name="NGS: QC and manipulation"><label id="illumina" text="Illumina data" /><label id="454" text="Roche-454 data" />
- <tool file="metag_tools/short_reads_figure_score.xml" />
- <tool file="metag_tools/short_reads_trim_seq.xml" /><label id="solid" text="AB-SOLiD data" /><tool file="next_gen_conversion/solid2fastq.xml" /><tool file="solid_tools/solid_qual_stats.xml" />
@@ -153,8 +135,6 @@
<section id="ngs_mapping" name="NGS: Mapping"><label id="illumina" text="Illumina" /><label id="roche_454" text="Roche-454" />
- <tool file="metag_tools/megablast_wrapper.xml" />
- <tool file="metag_tools/megablast_xml_parser.xml" /><label id="ab_solid" text="AB-SOLiD" /></section><section id="samtools" name="NGS: SAM Tools">
diff -r c559805d44df064f98dfbc94b59edba7be01adb9 -r 175bacc005a1437bfeedc8c76fe757467c08a870 tool_conf.xml.sample
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -68,13 +68,11 @@
<tool file="filters/axt_to_fasta.xml" /><tool file="filters/axt_to_lav.xml" /><tool file="filters/bed2gff.xml" />
- <tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="filters/gff2bed.xml" /><tool file="filters/lav_to_bed.xml" /><tool file="maf/maf_to_bed.xml" /><tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" />
- <tool file="fasta_tools/tabular_to_fasta.xml" /><tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" />
@@ -105,9 +103,6 @@
<tool file="filters/wiggle_to_simple.xml" /><tool file="stats/aggregate_binned_scores_in_intervals.xml" /></section>
- <section id="bxops" name="Operate on Genomic Intervals">
- <tool file="annotation_profiler/annotation_profiler.xml" />
- </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" />
@@ -130,12 +125,6 @@
<tool file="maf/vcf_to_maf_customtrack.xml" /><tool file="mutation/visualize.xml" /></section>
- <section id="multVar" name="Multivariate Analysis">
- <tool file="multivariate_stats/pca.xml" />
- <tool file="multivariate_stats/cca.xml" />
- <tool file="multivariate_stats/kpca.xml" />
- <tool file="multivariate_stats/kcca.xml" />
- </section><section id="hyphy" name="Evolution"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" />
@@ -144,15 +133,6 @@
<tool file="meme/meme.xml" /><tool file="meme/fimo.xml" /></section>
- <section id="clustal" name="Multiple Alignments">
- </section>
- <section id="fasta_manipulation" name="FASTA manipulation">
- <tool file="fasta_tools/fasta_compute_length.xml" />
- <tool file="fasta_tools/fasta_filter_by_length.xml" />
- <tool file="fasta_tools/fasta_concatenate_by_species.xml" />
- <tool file="fasta_tools/fasta_to_tabular.xml" />
- <tool file="fasta_tools/tabular_to_fasta.xml" />
- </section><section id="NGS_QC" name="NGS: QC and manipulation"><label id="fastqcsambam" text="FastQC: fastq/sam/bam" />
@@ -160,9 +140,6 @@
<label id="illumina" text="Illumina fastq" /><label id="454" text="Roche-454 data" />
- <tool file="metag_tools/short_reads_figure_score.xml" />
- <tool file="metag_tools/short_reads_trim_seq.xml" />
-
<label id="solid" text="AB-SOLiD data" /><tool file="next_gen_conversion/solid2fastq.xml" /><tool file="solid_tools/solid_qual_stats.xml" />
@@ -185,8 +162,6 @@
--><section id="solexa_tools" name="NGS: Mapping"><tool file="sr_mapping/bfast_wrapper.xml" />
- <tool file="metag_tools/megablast_wrapper.xml" />
- <tool file="metag_tools/megablast_xml_parser.xml" /><tool file="sr_mapping/PerM.xml" /><tool file="sr_mapping/srma_wrapper.xml" /><tool file="sr_mapping/mosaik.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0