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/
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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
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/
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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
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/
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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
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/
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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/
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0
12 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.
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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 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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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div 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n=this;this.$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 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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,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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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 (<1k)",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=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new 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e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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","highcharts_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 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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/
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commit/galaxy-central: guerler: Charts: Finalize box plots, add axes labels, series labels, grid options
by commits-noreply＠bitbucket.org 12 Jun '14
by commits-noreply＠bitbucket.org 12 Jun '14
12 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/
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12 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/
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commit/galaxy-central: davebgx: Fix call to get_repository_metadata_by_changeset_revision.
by commits-noreply＠bitbucket.org 12 Jun '14
by commits-noreply＠bitbucket.org 12 Jun '14
12 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/
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commit/galaxy-central: davebgx: Fix server error when importing a capsule.
by commits-noreply＠bitbucket.org 12 Jun '14
by commits-noreply＠bitbucket.org 12 Jun '14
12 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/
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