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June 2014

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commit/galaxy-central: natefoo: Merge stable.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a19ef9da5e47/ Changeset: a19ef9da5e47 User: natefoo Date: 2014-06-12 16:00:39 Summary: Merge stable. Affected #: 2 files diff -r 5d5ed9cbbf9b6a37dbf0777cf4b88015df9135f4 -r a19ef9da5e470d14a31ad8385f14168a14556224 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -128,6 +128,7 @@ from galaxy.util import heartbeat if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( fname=self.config.heartbeat_log ) + self.heartbeat.daemon = True self.heartbeat.start() # Enable the memdump signal catcher if configured and available if self.config.use_memdump: @@ -150,6 +151,7 @@ self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), galaxy.queue_worker.control_message_to_task) + self.control_worker.daemon = True self.control_worker.start() def shutdown( self ): 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: natefoo: Daemonize threads so that SIGINT (Ctrl-C) works again.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d6b1ea3a6a9e/ Changeset: d6b1ea3a6a9e Branch: stable User: natefoo Date: 2014-06-12 15:53:37 Summary: Daemonize threads so that SIGINT (Ctrl-C) works again. Affected #: 1 file diff -r 5a9adea86d411348023b7307b3c935cd99c6dea9 -r d6b1ea3a6a9ed2e7c3fa41518c5a690ed49c1265 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -128,6 +128,7 @@ from galaxy.util import heartbeat if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( fname=self.config.heartbeat_log ) + self.heartbeat.daemon = True self.heartbeat.start() # Enable the memdump signal catcher if configured and available if self.config.use_memdump: @@ -150,6 +151,7 @@ self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), galaxy.queue_worker.control_message_to_task) + self.control_worker.daemon = True self.control_worker.start() def shutdown( self ): 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: natefoo: Drop threadframe for heartbeat (its functionality was integrated in sys in Python 2.5...)
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d5ed9cbbf9b/ Changeset: 5d5ed9cbbf9b User: natefoo Date: 2014-06-12 15:51:45 Summary: Drop threadframe for heartbeat (its functionality was integrated in sys in Python 2.5...) Affected #: 2 files diff -r 07df86dff47c924830c2912500af356180778162 -r 5d5ed9cbbf9b6a37dbf0777cf4b88015df9135f4 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -26,7 +26,6 @@ pysqlite = 2.5.6 python_lzo = 1.08_2.03_static PyYAML = 3.10 -threadframe = 0.2 guppy = 0.1.10 SQLAlchemy = 0.7.9 ; msgpack_python = 0.2.4 diff -r 07df86dff47c924830c2912500af356180778162 -r 5d5ed9cbbf9b6a37dbf0777cf4b88015df9135f4 lib/galaxy/util/heartbeat.py --- a/lib/galaxy/util/heartbeat.py +++ b/lib/galaxy/util/heartbeat.py @@ -1,182 +1,167 @@ +import threading +import time +import traceback +import os +import sys -# Attempt to load threadframe module, and only define Heartbeat class -# if available +def get_current_thread_object_dict(): + """ + Get a dictionary of all 'Thread' objects created via the threading + module keyed by thread_id. Note that not all interpreter threads + have a thread objects, only the main thread and any created via the + 'threading' module. Threads created via the low level 'thread' module + will not be in the returned dictionary. -try: + HACK: This mucks with the internals of the threading module since that + module does not expose any way to match 'Thread' objects with + intepreter thread identifiers (though it should). + """ + rval = dict() + # Acquire the lock and then union the contents of 'active' and 'limbo' + # threads into the return value. + threading._active_limbo_lock.acquire() + rval.update( threading._active ) + rval.update( threading._limbo ) + threading._active_limbo_lock.release() + return rval - import pkg_resources - pkg_resources.require( "threadframe" ) +class Heartbeat( threading.Thread ): + """ + Thread that periodically dumps the state of all threads to a file + """ + def __init__( self, name="Heartbeat Thread", period=20, fname="heartbeat.log" ): + threading.Thread.__init__( self, name=name ) + self.should_stop = False + self.period = period + self.fname = fname + self.file = None + self.fname_nonsleeping = fname + ".nonsleeping" + self.file_nonsleeping = None + self.nonsleeping_heartbeats = { } + # Save process id + self.pid = os.getpid() + # Event to wait on when sleeping, allows us to interrupt for shutdown + self.wait_event = threading.Event() + def run( self ): + self.file = open( self.fname, "a" ) + print >> self.file, "Heartbeat for pid %d thread started at %s" % ( self.pid, time.asctime() ) + print >> self.file + self.file_nonsleeping = open ( self.fname_nonsleeping, "a" ) + print >> self.file_nonsleeping, "Non-Sleeping-threads for pid %d thread started at %s" % ( self.pid, time.asctime() ) + print >> self.file_nonsleeping + try: + while not self.should_stop: + # Print separator with timestamp + print >> self.file, "Traceback dump for all threads at %s:" % time.asctime() + print >> self.file + # Print the thread states + threads = get_current_thread_object_dict() + for thread_id, frame in sys._current_frames().iteritems(): + if thread_id in threads: + object = repr( threads[thread_id] ) + else: + object = "<No Thread object>" + print >> self.file, "Thread %s, %s:" % ( thread_id, object ) + print >> self.file + traceback.print_stack( frame, file=self.file ) + print >> self.file + print >> self.file, "End dump" + print >> self.file + self.file.flush() + self.print_nonsleeping(threads) + # Sleep for a bit + self.wait_event.wait( self.period ) + finally: + print >> self.file, "Heartbeat for pid %d thread stopped at %s" % ( self.pid, time.asctime() ) + print >> self.file + # Cleanup + self.file.close() + self.file_nonsleeping.close() -except: + def shutdown( self ): + self.should_stop = True + self.wait_event.set() + self.join() - import sys - print >> sys.stderr, "No threadframe module, Heartbeat not available" - Heartbeat = None + def thread_is_sleeping ( self, last_stack_frame ): + """ + Returns True if the given stack-frame represents a known + sleeper function (at least in python 2.5) + """ + _filename = last_stack_frame[0] + _line = last_stack_frame[1] + _funcname = last_stack_frame[2] + _text = last_stack_frame[3] + ### Ugly hack to tell if a thread is supposedly sleeping or not + ### These are the most common sleeping functions I've found. + ### Is there a better way? (python interpreter internals?) + ### Tested only with python 2.5 + if _funcname=="wait" and _text=="waiter.acquire()": + return True + if _funcname=="wait" and _text=="_sleep(delay)": + return True + if _funcname=="accept" and _text[-14:]=="_sock.accept()": + return True + if _funcname=="monitor" and _text.startswith("time.sleep( ") and _text.endswith(" )"): + return True + if _funcname=="drain_events" and _text=="sleep(polling_interval)": + return True + #Ugly hack: always skip the heartbeat thread + #TODO: get the current thread-id in python + # skip heartbeat thread by thread-id, not by filename + if _filename.find("/lib/galaxy/util/heartbeat.py")!=-1: + return True + ## By default, assume the thread is not sleeping + return False -else: + def get_interesting_stack_frame ( self, stack_frames ): + """ + Scans a given backtrace stack frames, returns a single + quadraple of [filename, line, function-name, text] of + the single, deepest, most interesting frame. - import threading - import threadframe - import time - import traceback - import os - import sys + Interesting being:: - def get_current_thread_object_dict(): + inside the galaxy source code ("/lib/galaxy"), + prefreably not an egg. """ - Get a dictionary of all 'Thread' objects created via the threading - module keyed by thread_id. Note that not all interpreter threads - have a thread objects, only the main thread and any created via the - 'threading' module. Threads created via the low level 'thread' module - will not be in the returned dictionary. + for _filename, _line, _funcname, _text in reversed(stack_frames): + idx = _filename.find("/lib/galaxy/") + if idx!=-1: + relative_filename = _filename[idx:] + return ( relative_filename, _line, _funcname, _text ) + # no "/lib/galaxy" code found, return the innermost frame + return stack_frames[-1] - HACK: This mucks with the internals of the threading module since that - module does not expose any way to match 'Thread' objects with - intepreter thread identifiers (though it should). - """ - rval = dict() - # Acquire the lock and then union the contents of 'active' and 'limbo' - # threads into the return value. - threading._active_limbo_lock.acquire() - rval.update( threading._active ) - rval.update( threading._limbo ) - threading._active_limbo_lock.release() - return rval + def print_nonsleeping( self, threads_object_dict ): + print >> self.file_nonsleeping, "Non-Sleeping threads at %s:" % time.asctime() + print >> self.file_nonsleeping + all_threads_are_sleeping = True + threads = get_current_thread_object_dict() + for thread_id, frame in sys._current_frames().iteritems(): + if thread_id in threads: + object = repr( threads[thread_id] ) + else: + object = "<No Thread object>" + tb = traceback.extract_stack(frame) + if self.thread_is_sleeping(tb[-1]): + if thread_id in self.nonsleeping_heartbeats: + del self.nonsleeping_heartbeats[thread_id] + continue - class Heartbeat( threading.Thread ): - """ - Thread that periodically dumps the state of all threads to a file using - the `threadframe` extension - """ - def __init__( self, name="Heartbeat Thread", period=20, fname="heartbeat.log" ): - threading.Thread.__init__( self, name=name ) - self.should_stop = False - self.period = period - self.fname = fname - self.file = None - self.fname_nonsleeping = fname + ".nonsleeping" - self.file_nonsleeping = None - self.nonsleeping_heartbeats = { } - # Save process id - self.pid = os.getpid() - # Event to wait on when sleeping, allows us to interrupt for shutdown - self.wait_event = threading.Event() - def run( self ): - self.file = open( self.fname, "a" ) - print >> self.file, "Heartbeat for pid %d thread started at %s" % ( self.pid, time.asctime() ) - print >> self.file - self.file_nonsleeping = open ( self.fname_nonsleeping, "a" ) - print >> self.file_nonsleeping, "Non-Sleeping-threads for pid %d thread started at %s" % ( self.pid, time.asctime() ) - print >> self.file_nonsleeping - try: - while not self.should_stop: - # Print separator with timestamp - print >> self.file, "Traceback dump for all threads at %s:" % time.asctime() - print >> self.file - # Print the thread states - threads = get_current_thread_object_dict() - for thread_id, frame in threadframe.dict().iteritems(): - if thread_id in threads: - object = repr( threads[thread_id] ) - else: - object = "<No Thread object>" - print >> self.file, "Thread %s, %s:" % ( thread_id, object ) - print >> self.file - traceback.print_stack( frame, file=self.file ) - print >> self.file - print >> self.file, "End dump" - print >> self.file - self.file.flush() - self.print_nonsleeping(threads) - # Sleep for a bit - self.wait_event.wait( self.period ) - finally: - print >> self.file, "Heartbeat for pid %d thread stopped at %s" % ( self.pid, time.asctime() ) - print >> self.file - # Cleanup - self.file.close() - self.file_nonsleeping.close() + # Count non-sleeping thread heartbeats + if thread_id in self.nonsleeping_heartbeats: + self.nonsleeping_heartbeats[thread_id] += 1 + else: + self.nonsleeping_heartbeats[thread_id]=1 - def shutdown( self ): - self.should_stop = True - self.wait_event.set() - self.join() + good_frame = self.get_interesting_stack_frame(tb) + print >> self.file_nonsleeping, "Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n File %s:%d\n Function \"%s\"\n %s" % \ + ( thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3] ) + all_threads_are_sleeping = False - def thread_is_sleeping ( self, last_stack_frame ): - """ - Returns True if the given stack-frame represents a known - sleeper function (at least in python 2.5) - """ - _filename = last_stack_frame[0] - _line = last_stack_frame[1] - _funcname = last_stack_frame[2] - _text = last_stack_frame[3] - ### Ugly hack to tell if a thread is supposedly sleeping or not - ### These are the most common sleeping functions I've found. - ### Is there a better way? (python interpreter internals?) - ### Tested only with python 2.5 - if _funcname=="wait" and _text=="waiter.acquire()": - return True - if _funcname=="wait" and _text=="_sleep(delay)": - return True - if _funcname=="accept" and _text[-14:]=="_sock.accept()": - return True - #Ugly hack: always skip the heartbeat thread - #TODO: get the current thread-id in python - # skip heartbeat thread by thread-id, not by filename - if _filename.find("/lib/galaxy/util/heartbeat.py")!=-1: - return True - ## By default, assume the thread is not sleeping - return False + if all_threads_are_sleeping: + print >> self.file_nonsleeping, "All threads are sleeping." + print >> self.file_nonsleeping + self.file_nonsleeping.flush() - def get_interesting_stack_frame ( self, stack_frames ): - """ - Scans a given backtrace stack frames, returns a single - quadraple of [filename, line, function-name, text] of - the single, deepest, most interesting frame. - - Interesting being:: - - inside the galaxy source code ("/lib/galaxy"), - prefreably not an egg. - """ - for _filename, _line, _funcname, _text in reversed(stack_frames): - idx = _filename.find("/lib/galaxy/") - if idx!=-1: - relative_filename = _filename[idx:] - return ( relative_filename, _line, _funcname, _text ) - # no "/lib/galaxy" code found, return the innermost frame - return stack_frames[-1] - - def print_nonsleeping( self, threads_object_dict ): - print >> self.file_nonsleeping, "Non-Sleeping threads at %s:" % time.asctime() - print >> self.file_nonsleeping - all_threads_are_sleeping = True - threads = get_current_thread_object_dict() - for thread_id, frame in threadframe.dict().iteritems(): - if thread_id in threads: - object = repr( threads[thread_id] ) - else: - object = "<No Thread object>" - tb = traceback.extract_stack(frame) - if self.thread_is_sleeping(tb[-1]): - if thread_id in self.nonsleeping_heartbeats: - del self.nonsleeping_heartbeats[thread_id] - continue - - # Count non-sleeping thread heartbeats - if thread_id in self.nonsleeping_heartbeats: - self.nonsleeping_heartbeats[thread_id] += 1 - else: - self.nonsleeping_heartbeats[thread_id]=1 - - good_frame = self.get_interesting_stack_frame(tb) - print >> self.file_nonsleeping, "Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n File %s:%d\n Function \"%s\"\n %s" % \ - ( thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3] ) - all_threads_are_sleeping = False - - if all_threads_are_sleeping: - print >> self.file_nonsleeping, "All threads are sleeping." - print >> self.file_nonsleeping - self.file_nonsleeping.flush() - Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #415)
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a9adea86d41/ Changeset: 5a9adea86d41 Branch: stable User: natefoo Date: 2014-06-12 14:50:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #415) [stable] API bug fixes for stable Affected #: 2 files diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset" ), + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -156,7 +156,7 @@ output_dict[ 'output_name' ] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) - for job in vars[ 'jobs' ]: + for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) for output_name, collection_instance in vars.get( 'implicit_collections', {} ).iteritems(): 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: 3 new changesets
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddddb19cb1bf/ Changeset: ddddb19cb1bf Branch: stable User: jmchilton Date: 2014-06-11 19:37:24 Summary: Modify url_for in history_contents.py. No clue why - but this randomly fails on main. Will keep looking into it - but it wasn't really giving the pretty URL I wanted anyway (though it was working and this still works due to backward compatbility on this route). Affected #: 1 file diff -r 0af48b3c8f33fbe0f05e775f98a14761804c7ac5 -r ddddb19cb1bf2c12aa4d6f824b7a850d4c858e2c lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset" ), + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): https://bitbucket.org/galaxy/galaxy-central/commits/f7be4e7782c1/ Changeset: f7be4e7782c1 Branch: stable User: dannon Date: 2014-06-11 17:39:21 Summary: Correct tools handling of tool.handle_input -- this doesn't always return a successful job. Affected #: 1 file diff -r ddddb19cb1bf2c12aa4d6f824b7a850d4c858e2c -r f7be4e7782c1368a3c4a868c7c63989e11c151fd lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -156,7 +156,7 @@ output_dict[ 'output_name' ] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) - for job in vars[ 'jobs' ]: + for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) for output_name, collection_instance in vars.get( 'implicit_collections', {} ).iteritems(): https://bitbucket.org/galaxy/galaxy-central/commits/5a9adea86d41/ Changeset: 5a9adea86d41 Branch: stable User: natefoo Date: 2014-06-12 14:50:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #415) [stable] API bug fixes for stable Affected #: 2 files diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset" ), + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -156,7 +156,7 @@ output_dict[ 'output_name' ] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) - for job in vars[ 'jobs' ]: + for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) for output_name, collection_instance in vars.get( 'implicit_collections', {} ).iteritems(): 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: guerler: Charts: Pack scripts
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/07df86dff47c/ Changeset: 07df86dff47c User: guerler Date: 2014-06-12 00:55:14 Summary: Charts: Pack scripts Affected #: 3 files diff -r 7ac55136509c9c43964dc0d3a773d85e680a93ea -r 07df86dff47c924830c2912500af356180778162 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. -define("mvc/ui/ui-modal",[],function(){var 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r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa 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e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","mvc/ui/ui-modal"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" 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'+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=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="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),a=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),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="ui-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:{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(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="ui-button-menu '+e.cls+'">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:i,Button:s,Icon:o,ButtonIcon:u,Input:h,Anchor:a,Message:f,Searchbox:l,Select:t,ButtonMenu:c,Modal:n,Textarea:p,Image:r,RadioButton:d}}),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=t.definition;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(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=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]||a==="auto")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.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_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(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){e.find("svg").length>0?r(e,t,i):n(e)}function n(e){e.find("#canvas").jqplotSaveImage({})}function r(e,t,n){var r=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);i(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),e.find(".highcharts-button").hide(),o+=r.serializeToString(this),e.find(".highcharts-button").show()}),s(e,t,{filename:n||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function i(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function s(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find(".charts-viewport-container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info"));var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning"),t.hide();break;default:r.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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_definition=e.definition;var i=this.chart_definition.use_panels||e.settings.get("use_panels")==="true",s=1;i&&(s=e.groups.length),this._createContainer(this.chart_definition.tag,s),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_definition.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_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=r.merge({index:e.get(o)},u)}t.groups.push({key:++n+":"+e.get("key"),columns:s})}),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","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"SVGs are converted to PDF via "+o.app.config.get("screenshot_url")+" and CANVAS-based charts to PNG-files.",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll: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.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=[],f=n[e];o&&a.push({label:"Column: Row Number",value:"auto"});var l=t.metadata_column_types;for(var c in l){var h=!1;l[c]=="int"||l[c]=="float"?h=u:h=s,h&&a.push({label:"Column: "+(parseInt(c)+1)+" ["+l[c]+"]",value:c})}f.update(a);if(!f.exists(this.group.get(e))){var p=f.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+p+'".'),this.group.set(e,p)}f.value(this.group.get(e)),f.setOnChange(function(t){i.group.set(e,t),i.chart.set("modified",!0)}),f.show()},_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({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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i=n.pos[0]+(r.offsetLeft||0),o=n.pos[1]+(r.offsetTop||0),f=s.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?u:a).tickFormat()(t.y()(n.point,n.pointIndex)),c=N(n.series.key,f,l,n,B);e.tooltip.show([i,o],c,n.value<0?"n":"s",null,r)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+p.left,e.pos[1]+p.top],D.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){D.tooltipHide(e)}),r.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+p.left,e.pos[1]+p.top],D.tooltipShow(e)}),r.dispatch.on("elementMouseout.tooltip",function(e){D.tooltipHide(e)}),D.on("tooltipHide",function(){T&&e.tooltip.cleanup()}),B.dispatch=D,B.legend=c,B.lines=t,B.lines2=n,B.bars=r,B.bars2=i,B.xAxis=s,B.x2Axis=o,B.y1Axis=u,B.y2Axis=a,B.y3Axis=f,B.y4Axis=l,d3.rebind(B,t,"defined","size","clipVoronoi","interpolate"),B.options=e.utils.optionsFunc.bind(B),B.x=function(e){return arguments.length?(y=e,t.x(e),r.x(e),B):y},B.y=function(e){return 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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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(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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]||a==="auto")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},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;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));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,100),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(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.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_definition.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_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error(r)}}function r(e){var t=e.$el,n=e.url,r=e.name,o=new XMLSerializer,u="",a=this,f=0,l=0;return t.find("svg").each(function(){var e=$(this);i(e),f=parseInt(e.css("height")),l=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:l,height:f}),e.find(".highcharts-button").hide(),u+=o.serializeToString(this),e.find(".highcharts-button").show()}),s(t,n,{filename:r||"chart",type:"application/pdf",height:f,width:l,scale:2,svg:u}),u}function i(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function s(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"SVGs are converted to PDF via "+o.app.config.get("screenshot_url")+" and CANVAS-based charts to PNG-files.",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create({$el:o.viewport_view.$el,url:o.app.config.get("screenshot_url"),title:o.chart.get("title"),error:function(e){o.message.update({message:"Please reduce your chart to a single panel and try again.",status:"danger"})}})})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll: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.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f);if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}a?l.value(this.chart.groups.first().get(e)):l.value(this.group.get(e)),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_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({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" ("+i.library+")",url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100,screenshot_url:"http://export.highcharts.com/"}})}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),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/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m){return Backbone.Model.extend({defaults:{jqplot_bar:p,nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f,jqplot_line:d,jqplot_scatter:v,jqplot_boxplot:m}})}),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()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 7ac55136509c9c43964dc0d3a773d85e680a93ea -r 07df86dff47c924830c2912500af356180778162 config/plugins/visualizations/charts/static/library/screenshot.js --- a/config/plugins/visualizations/charts/static/library/screenshot.js +++ b/config/plugins/visualizations/charts/static/library/screenshot.js @@ -1,26 +1,40 @@ -/** - * Screenshot creator -*/ - // dependencies define(["libs/underscore"], function(_) { // screenshot - function create ($el, screenshot_url, name) { - if ($el.find('svg').length > 0) { - _fromSVG ($el, screenshot_url, name); + function create (options) { + if (options.$el.find('svg').length > 0) { + _fromSVG (options); } else { - _fromCanvas ($el); + _fromCanvas (options); } }; // from jqplot - function _fromCanvas ($el) { - $el.find('.charts-viewport-canvas').jqplotSaveImage({}); + function _fromCanvas (options) { + try { + var $canvas = options.$el.find('.jqplot-target'); + var imgData = $canvas.jqplotToImageStr({}); + if (imgData) { + window.location.href = imgData.replace('image/png', 'image/octet-stream'); + } + } catch (err) { + console.debug('FAILED - Screenshot::_fromCanvas() - ' + err); + if (options.error) { + options.error(err); + } + } }; // from svg - function _fromSVG ($el, screenshot_url, name) { + function _fromSVG (options) { + + // get parameters + var $el = options.$el; + var screenshot_url = options.url; + var name = options.name; + + // serialize svg var serializer = new XMLSerializer(); var xmlString = ''; var self = this; diff -r 7ac55136509c9c43964dc0d3a773d85e680a93ea -r 07df86dff47c924830c2912500af356180778162 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -48,7 +48,14 @@ onclick : function() { // attempt to load chart editor self._wait (self.chart, function() { - Screenshot.create(self.viewport_view.$el, self.app.config.get('screenshot_url'), self.chart.get('title')); + Screenshot.create({ + $el : self.viewport_view.$el, + url : self.app.config.get('screenshot_url'), + title : self.chart.get('title'), + error : function(err) { + self.message.update({ message: 'Please reduce your chart to a single panel and try again.', status: 'danger' }); + } + }); }); } }) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Finalize box plots, add axes labels, series labels, grid options
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ac55136509c/ Changeset: 7ac55136509c User: guerler Date: 2014-06-11 23:40:40 Summary: Charts: Finalize box plots, add axes labels, series labels, grid options Affected #: 12 files diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -17,7 +17,7 @@ process_id : process_id, chart : chart, request_dictionary : request_dictionary, - makeConfig : function(plot_config){ + makeConfig : function(groups, plot_config){ $.extend(true, plot_config, { seriesDefaults: { renderer : $.jqplot.BarRenderer diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js @@ -6,7 +6,7 @@ library : 'jqPlot', tag : 'div', execute : 'boxplot', - keywords : 'default large', + keywords : 'small medium large', columns : { y : { title : 'Observations', @@ -14,123 +14,8 @@ } }, 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' - }, - 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' - } - ] - }, - y_axis_grid : { - title : 'Axis grid', - info : 'Would you like to show grid lines for this axis?', - type : 'radiobutton', - init : '1', - data : [ - { - label : 'On', - value : '1' - }, - { - label : 'Off', - value : '0' - } - ] + show_legend : { + init : 'false' } } }); diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -19,17 +19,16 @@ group.columns = null; group.columns = { x: { - index : index++ + index: index++ } } } - var plot = new Plot(this.app, this.options); plot.draw({ process_id : process_id, chart : chart, request_dictionary : request_dictionary, - makeConfig : function(plot_config, groups){ + makeConfig : function(groups, plot_config){ var boundary = Tools.getDomains(groups, 'x'); $.extend(true, plot_config, { seriesDefaults: { @@ -42,7 +41,8 @@ }, axes : { xaxis: { - pad: 1.2 + min: -1, + max: groups.length + 0.01 }, yaxis: { min: boundary.x.min, @@ -51,7 +51,29 @@ } }); }, - makeSeries : function (groups) { + makeCategories: function(groups) { + // define custom category labels + var x_labels = []; + for (var group_index in groups) { + x_labels.push(groups[group_index].key); + } + + // use default mapping + Tools.mapCategories (groups, x_labels); + + // return labels array for x axis + return { + array: { + x : x_labels + } + } + }, + makeSeriesLabels : function (groups, plot_config) { + return [{ + label: 'Boxplot values' + }]; + }, + makeSeries: function (groups) { /* example data var catOHLC = [ [0, 138.7, 139.68, 135.18, 135.4], @@ -72,14 +94,14 @@ } // loop through data groups - for (var group_index in request_dictionary.groups) { + var indeces = [2, 4, 0, 1]; + for (var group_index in groups) { // get group - var group = request_dictionary.groups[group_index]; + var group = groups[group_index]; // format chart data var point = []; point.push(parseInt(group_index)); - var indeces = [2, 4, 0, 1]; for (var key in indeces) { point.push(group.values[indeces[key]].x); } @@ -88,6 +110,14 @@ plot_data.push (point); } + // HACK: the boxplot renderer has an issue with single elements + var point = []; + point[0] = plot_data.length; + for (var key in indeces) { + point.push(0); + } + plot_data.push (point); + // return return [plot_data]; } diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -100,6 +100,22 @@ ] }, + x_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for this axis?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + }, separator_tick : { title : 'Y axis', type : 'separator' @@ -192,6 +208,22 @@ ] }, + y_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for this axis?', + type : 'radiobutton', + init : 'true', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + }, separator_legend : { title : 'Others', type : 'separator' diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js @@ -57,11 +57,6 @@ } }, - // Custom labels for the series are specified with the "label" - // option on the series option. Here a series option object - // is specified for each series. - series: [], - axesDefaults: { labelRenderer : $.jqplot.CanvasAxisLabelRenderer, labelOptions: { @@ -76,25 +71,22 @@ }, axes: { - // Use a category axis on the x axis and use our custom ticks. xaxis: { label : chart.settings.get('x_axis_label'), tickRenderer : $.jqplot.CanvasAxisTickRenderer, tickOptions: { - angle : -30 + angle : chart.settings.get('use_panels') === 'true' ? 0 : -30, + showGridline : chart.settings.get('x_axis_grid') === 'true' }, tickInterval : 1, pad : 0 }, - // Pad the y axis just a little so bars can get close to, but - // not touch, the grid boundaries. 1.2 is the default padding. yaxis: { label : chart.settings.get('y_axis_label'), - tickOptions : {}, + tickOptions : { + showGridline : chart.settings.get('y_axis_grid') === 'true' + }, pad : 0 - //tickOptions : {formatString: '$%d'}, - //padding : 1.2, - //autoscale:true } }, @@ -110,17 +102,17 @@ showTooltip : false, style : 'pointer' }, + highlighter: { show : true, showMarker : false, tooltipAxes : 'xy' - } + }, + + series: [] }; - // Show the legend and put it outside the grid, but inside the - // plot container, shrinking the grid to accomodate the legend. - // A value of "outside" would not shrink the grid and allow - // the legend to overflow the container. + // Show the legend and put it outside the grid if (chart.settings.get('show_legend') == 'true') { plot_config.legend = { renderer : $.jqplot.EnhancedLegendRenderer, diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js @@ -38,10 +38,11 @@ // draw all data into a single canvas render: function(canvas_id, groups) { // get parameters - var chart = this.options.chart; - var makeCategories = this.options.makeCategories; - var makeSeries = this.options.makeSeries; - var makeConfig = this.options.makeConfig; + var chart = this.options.chart; + var makeCategories = this.options.makeCategories; + var makeSeries = this.options.makeSeries; + var makeSeriesLabels = this.options.makeSeriesLabels; + var makeConfig = this.options.makeConfig; // create configuration var plot_config = configmaker(chart); @@ -50,18 +51,25 @@ // draw plot try { // make custom categories call - this._makeAxes(plot_config, groups, chart.settings); + this._makeAxes(groups, plot_config, chart.settings); // make custom series call if (makeSeries) { - plot_data = makeSeries(groups); + plot_config.series = makeSeriesLabels(groups, plot_config); + } else { + plot_config.series = this._makeSeriesLabels(groups); + } + + // make custom series call + if (makeSeries) { + plot_data = makeSeries(groups, plot_config); } else { plot_data = Tools.makeSeries(groups); } // make custom config call if (makeConfig) { - makeConfig(plot_config, groups); + makeConfig(groups, plot_config); } // check chart state @@ -96,8 +104,19 @@ } }, + // make series labels + _makeSeriesLabels: function(groups, plot_config) { + var series = []; + for (var group_index in groups) { + series.push({ + label: groups[group_index].key + }); + } + return series; + }, + // create axes formatting - _makeAxes: function(plot_config, groups, settings) { + _makeAxes: function(groups, plot_config, settings) { // result var makeCategories = this.options.makeCategories; var categories; diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js @@ -12,6 +12,11 @@ title : 'Values for y-axis', is_numeric : true } + }, + settings : { + x_axis_grid : { + init : 'true' + } } }); diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js @@ -17,7 +17,7 @@ process_id : process_id, chart : chart, request_dictionary : request_dictionary, - makeConfig : function(plot_config){ + makeConfig : function(groups, plot_config){ $.extend(true, plot_config, { seriesDefaults: { renderer: $.jqplot.LineRenderer, diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js @@ -62,6 +62,11 @@ makeConfig(d3chart); } + // hide controls if in multi-viewer mode + if (chart.settings.get('use_panels') === 'true') { + d3chart.options({showControls: false}); + } + // hide min/max values d3chart.xAxis.showMaxMin(false); d3chart.yAxis.showMaxMin(chart.definition.showmaxmin); diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/tools.js --- a/config/plugins/visualizations/charts/static/charts/tools.js +++ b/config/plugins/visualizations/charts/static/charts/tools.js @@ -22,7 +22,7 @@ request_dictionary.success = function() { try { // check if this chart has multiple panels - if (chart.definition.use_panels || chart.settings.get('use_panels') === 'true') { + if (chart.settings.get('use_panels') === 'true') { // draw groups in separate panels var valid = true; for (var group_index in request_dictionary.groups) { @@ -131,7 +131,6 @@ // append series plot_data.push(data); } - // return return plot_data; @@ -163,6 +162,17 @@ } // index all values contained in label columns (for all groups) + mapCategories(array, groups); + + // return dictionary + return { + array : array + } +}; + +// apply default mapping +// index all values contained in label columns (for all groups) +function mapCategories(array, groups) { for (var i in groups) { var group = groups[i]; for (var j in group.values) { @@ -172,15 +182,10 @@ } } } - - // return dictionary - return { - array : array - } }; // category make for unique category labels -function makeCategoriesUnique(groups, with_index) { +function makeUniqueCategories(groups, with_index) { // hashkeys, arrays and counter for labeled columns var categories = {}; var array = {}; @@ -247,7 +252,8 @@ panelHelper : panelHelper, makeCategories : makeCategories, makeSeries : makeSeries, - getDomains : getDomains + getDomains : getDomains, + mapCategories : mapCategories } }); \ No newline at end of file diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/library/screenshot.js --- a/config/plugins/visualizations/charts/static/library/screenshot.js +++ b/config/plugins/visualizations/charts/static/library/screenshot.js @@ -16,7 +16,7 @@ // from jqplot function _fromCanvas ($el) { - $el.find('#canvas').jqplotSaveImage({}); + $el.find('.charts-viewport-canvas').jqplotSaveImage({}); }; // from svg diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -1,6 +1,6 @@ // dependencies -define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'plugin/library/screenshot', 'utils/utils'], - function(Portlet, Ui, Screenshot, Utils) { +define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils'], + function(Portlet, Ui, Utils) { // widget return Backbone.View.extend({ @@ -134,12 +134,9 @@ // load chart settings this.chart_definition = chart.definition; - // read settings - var use_panels = this.chart_definition.use_panels || (chart.settings.get('use_panels') === 'true'); - // determine number of svg/div-elements to create var n_panels = 1; - if (use_panels) { + if (chart.settings.get('use_panels') === 'true') { n_panels = chart.groups.length; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Merge stable.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/23b8a52409a4/ Changeset: 23b8a52409a4 User: davebgx Date: 2014-06-11 23:00:56 Summary: Merge stable. Affected #: 1 file diff -r 651c1ed8e4d35cc140d20038c17e33eeb4381804 -r 23b8a52409a41e13a8869b51a7360e4040537579 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -24,26 +24,27 @@ name, owner = name_owner if not ok: repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - # Do not allow the repository to be automatically installed if population resulted in errors. - tip_changeset_revision = repository.tip( trans.app ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, - trans.security.encode_id( repository.id ), - tip_changeset_revision ) - if repository_metadata: - if repository_metadata.downloadable: - repository_metadata.downloadable = False - trans.sa_session.add( repository_metadata ) - if not flush: - flush = True - # Do not allow dependent repository revisions to be automatically installed if population - # resulted in errors. - dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata ) - for dependent_downloadable_revision in dependent_downloadable_revisions: - if dependent_downloadable_revision.downloadable: - dependent_downloadable_revision.downloadable = False - trans.sa_session.add( dependent_downloadable_revision ) + if repository is not None: + # Do not allow the repository to be automatically installed if population resulted in errors. + tip_changeset_revision = repository.tip( trans.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, + trans.security.encode_id( repository.id ), + tip_changeset_revision ) + if repository_metadata: + if repository_metadata.downloadable: + repository_metadata.downloadable = False + trans.sa_session.add( repository_metadata ) if not flush: flush = True + # Do not allow dependent repository revisions to be automatically installed if population + # resulted in errors. + dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata ) + for dependent_downloadable_revision in dependent_downloadable_revisions: + if dependent_downloadable_revision.downloadable: + dependent_downloadable_revision.downloadable = False + trans.sa_session.add( dependent_downloadable_revision ) + if not flush: + flush = True if flush: trans.sa_session.flush() 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: davebgx: Fix call to get_repository_metadata_by_changeset_revision.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ca53bc55bdc5/ Changeset: ca53bc55bdc5 Branch: stable User: davebgx Date: 2014-06-11 22:50:43 Summary: Fix call to get_repository_metadata_by_changeset_revision. Affected #: 1 file diff -r 4c58aa19a3d7ad94747d5b4dcfd031bebb37a35f -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -33,7 +33,7 @@ if repository is not None: # Do not allow the repository to be automatically installed if population resulted in errors. tip_changeset_revision = repository.tip( trans.app ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), tip_changeset_revision ) if repository_metadata: 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: davebgx: Fix server error when importing a capsule.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4c58aa19a3d7/ Changeset: 4c58aa19a3d7 Branch: stable User: davebgx Date: 2014-06-11 22:30:07 Summary: Fix server error when importing a capsule. Affected #: 1 file diff -r 0af48b3c8f33fbe0f05e775f98a14761804c7ac5 -r 4c58aa19a3d7ad94747d5b4dcfd031bebb37a35f lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -30,26 +30,27 @@ name, owner = name_owner if not ok: repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - # Do not allow the repository to be automatically installed if population resulted in errors. - tip_changeset_revision = repository.tip( trans.app ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - tip_changeset_revision ) - if repository_metadata: - if repository_metadata.downloadable: - repository_metadata.downloadable = False - trans.sa_session.add( repository_metadata ) - if not flush: - flush = True - # Do not allow dependent repository revisions to be automatically installed if population - # resulted in errors. - dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata ) - for dependent_downloadable_revision in dependent_downloadable_revisions: - if dependent_downloadable_revision.downloadable: - dependent_downloadable_revision.downloadable = False - trans.sa_session.add( dependent_downloadable_revision ) + if repository is not None: + # Do not allow the repository to be automatically installed if population resulted in errors. + tip_changeset_revision = repository.tip( trans.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, + trans.security.encode_id( repository.id ), + tip_changeset_revision ) + if repository_metadata: + if repository_metadata.downloadable: + repository_metadata.downloadable = False + trans.sa_session.add( repository_metadata ) if not flush: flush = True + # Do not allow dependent repository revisions to be automatically installed if population + # resulted in errors. + dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata ) + for dependent_downloadable_revision in dependent_downloadable_revisions: + if dependent_downloadable_revision.downloadable: + dependent_downloadable_revision.downloadable = False + trans.sa_session.add( dependent_downloadable_revision ) + if not flush: + flush = True if flush: trans.sa_session.flush() 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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