May 2014 - galaxy-commits - lists.galaxyproject.org

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

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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

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.

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commit/galaxy-central: dannon: Merge from next-stable.
by commits-noreply＠bitbucket.org 19 May '14

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.

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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

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

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

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

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 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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 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'+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 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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.

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commit/galaxy-central: dan: Fix for tool shed handling new GenomeBuilds manager.
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.

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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

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. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

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. 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