[galaxy-commits] commit/galaxy-central: 11 new changesets

16 Sep 2014

11 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/cadad49537de/
Changeset:   cadad49537de
User:        martenson
Date:        2014-09-08 18:27:49+00:00
Summary:     initial implementation of UI, API and flow for importing from Galaxy user directories, introduces jstree browser into the project, includes refactoring of some library API methods into common managers
Affected #:  22 files

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 lib/galaxy/util/dictobj.py

--- /dev/null
+++ b/lib/galaxy/util/dictobj.py
@@ -0,0 +1,229 @@
+import pickle
+
+class DictionaryObject(object):
+  """
+  A class that has all the functionality of a normal Python dictionary, except
+  for the fact it is itself immutable.  It also has the added feature of
+  being able to lookup values by using keys as attributes.
+
+  The reason for the class being immutable by default is to help make it a
+  little easier to use in multiprocessing situations.  Granted, the underlying
+  values themselves are not deeply copied, but the aim is to enforce some
+  ensurances of immutability on the container class.
+
+  When using positional arguments, the first argument must always be something
+  that would be a valid argument for a dict().  However, a second, optional
+  argument may be passed to create a default value when keys are not found.
+  
+  Examples:
+    >>> d = DictionaryObject({'a':1, 'b':True, 3:'x'})
+    >>> print d.a, d.b, d[3]
+    1 True x
+    
+    >>> d = DictionaryObject((('a',1),('b',2)))
+    >>> print d.a, d.b
+    1 2
+    
+    >>> d = DictionaryObject(a=1, b=True)
+    >>> print d
+    DictionaryObject({'a': 1, 'b': True})
+
+    >>> d = DictionaryObject({'a':1, 'b':True}, None)
+    >>> print d.a, d.b, d.c, d.d
+    1 True None None
+    
+    >>> d = DictionaryObject({'a':1}, None)
+    >>> m = MutableDictionaryObject(d)
+    >>> print d == m
+    True
+    >>> m.a = 0
+    >>> print d == m, d < m, d > m, d != m, d <= m, d >= m
+    False False True True False True
+  
+    >>> import pickle
+    >>> m1 = MutableDictionaryObject({'a':1}, None)
+    >>> m2 = pickle.loads(pickle.dumps(m1))
+    >>> print m1 == m2
+    True
+    >>> m1.a = 3
+    >>> print m1 == m2
+    False
+    >>> m1.a == 3
+    True
+    >>> m1['c'] = 5
+    >>> m1['c']
+    5
+    """
+  def __init__(self, contents=(), *args, **kwargs):
+    """
+    Take as input a dictionary-like object and return a DictionaryObject.
+    It also makes sure any keys containing dictionaries are also converted
+    to DictionaryObjects.
+    """
+    super(DictionaryObject, self).__init__()
+    if isinstance(contents, DictionaryObject):
+      self.__dict__.update(pickle.loads(pickle.dumps(contents.__dict__)))
+      return
+
+    self.__dict__['_items'] = dict(contents, **kwargs)
+
+    if len(args) > 1:
+      raise TypeError("too many arguments")
+
+    # If we have more than one argument passed in, use the second argument
+    # as a default value.
+    if args:
+      try:
+        default = type(self)(args[0])
+      except:
+        default = args[0]
+      self.__dict__['_defaultValue'] = default
+    else:
+      self.__dict__['_defaultValue'] = None
+    self.__dict__['_defaultIsSet'] = len(args) > 0
+
+    for k in self._items:
+      if isinstance(self._items[k], dict):
+        self._items[k] = type(self)(self._items[k])
+
+  def __setstate__(self, dict):
+    self.__dict__.update(dict)
+
+  def __getstate__(self):
+    return self.__dict__.copy()
+
+  def __getattr__(self, name):
+    """
+    This is the method that makes all the magic happen.  Search for
+    'name' in self._items and return the value if found.  If a default
+    value has been set and 'name' is not found in self._items, return it.
+    Otherwise raise an AttributeError.
+
+    Example:
+      >>> d = DictionaryObject({'keys':[1,2], 'values':3, 'x':1})
+      >>> d.keys
+      <bound method DictionaryObject.keys of DictionaryObject({'keys': [1, 2], 'x': 1, 'values': 3})>
+      >>> d.values
+      <bound method DictionaryObject.values of DictionaryObject({'keys': [1, 2], 'x': 1, 'values': 3})>
+      >>> d.x
+      1
+      >>> d['keys']
+      [1, 2]
+      >>> d['values']
+      3
+    """
+    if name in self._items:
+      return self._items[name]
+    if self._defaultIsSet:
+      return self._defaultValue
+    raise AttributeError("'%s' object has no attribute '%s'" % (type(self).__name__, name))
+
+  def __setattr__(self, name, value):
+    """
+    This class is immutable-by-default.  See MutableDictionaryObject.
+    """
+    raise AttributeError("'%s' object does not support assignment" % type(self).__name__)
+
+  def __getitem__(self, name):
+    return self._items[name]
+    
+  def __contains__(self, name):
+    return name in self._items
+    
+  def __len__(self):
+    return len(self._items)
+    
+  def __iter__(self):
+    return iter(self._items)
+      
+  def __repr__(self):
+    if self._defaultIsSet:
+      params = "%s, %s" % (repr(self._items), self._defaultValue)
+    else:
+      params = repr(self._items)
+    return "%s(%s)" % (type(self).__name__, params)
+    
+  def __cmp__(self, rhs):
+    if self < rhs:
+      return -1
+    if self > rhs:
+      return 1
+    return 0
+
+  def __eq__(self, rhs):
+    val = cmp(self._items, rhs._items)
+    if 0 == val:
+      return 0 == cmp(self._defaultValue, rhs._defaultValue)
+    return 0 == val
+
+  def __ne__(self, rhs):
+    return not (self == rhs)
+
+  def __lt__(self, rhs):
+    val = cmp(self._items, rhs._items)
+    if 0 == val:
+      return -1 == cmp(self._defaultValue, rhs._defaultValue)
+    return -1 == val
+
+  def __le__(self, rhs):
+    return self < rhs or self == rhs
+
+  def __gt__(self, rhs):
+    return not (self <= rhs)
+
+  def __ge__(self, rhs):
+    return self > rhs or self == rhs
+
+  def keys(self):
+    return self._items.keys()
+    
+  def values(self):
+    return self._items.values()
+
+  def asdict(self):
+    """
+    Copy the data back out of here and into a dict.  Then return it.
+    Some libraries may check specifically for dict objects, such
+    as the json library; so, this makes it convenient to get the data
+    back out.
+
+    >>> import dictobj
+    >>> d = {'a':1, 'b':2}
+    >>> dictobj.DictionaryObject(d).asdict() == d
+    True
+    >>> d['c'] = {1:2, 3:4}
+    >>> dictobj.DictionaryObject(d).asdict() == d
+    True
+    """
+    items = {}
+    for name in self._items:
+      value = self._items[name]
+      if isinstance(value, DictionaryObject):
+        items[name] = value.asdict()
+      else:
+        items[name] = value
+    return items
+
+class MutableDictionaryObject(DictionaryObject):
+  """
+  Slight enhancement of the DictionaryObject allowing one to add
+  attributes easily, in cases where that functionality is wanted.
+
+  Examples:
+    >>> d = MutableDictionaryObject({'a':1, 'b':True}, None)
+    >>> print d.a, d.b, d.c, d.d
+    1 True None None
+    >>> d.c = 3
+    >>> del d.a
+    >>> print d.a, d.b, d.c, d.d
+    None True 3 None
+  """
+  def __setattr__(self, name, value):
+    self._items[name] = value
+
+  def __delattr__(self, name):
+    del self._items[name]
+    
+  __setitem__ = __setattr__
+  __delitem__ = __delattr__
+  

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 lib/galaxy/util/jstree.py
--- /dev/null
+++ b/lib/galaxy/util/jstree.py
@@ -0,0 +1,173 @@
+import os
+import copy
+from galaxy.util import dictobj
+from collections import namedtuple
+
+Path = namedtuple('Path', ('path', 'id', 'options'))
+
+
+class Node(dictobj.DictionaryObject):
+  """
+  This class exists as a helper to the JSTree.  Its "jsonData" method can
+  generate sub-tree JSON without putting the logic directly into the JSTree.
+
+  This data structure is only semi-immutable.  The JSTree uses a directly
+  iterative (i.e. no stack is managed) builder pattern to construct a
+  tree out of paths.  Therefore, the children are not known in advance, and
+  we have to keep the children attribute mutable.
+  """
+
+  def __init__(self, path, oid, **kwargs):
+    """
+    kwargs allows users to pass arbitrary information into a Node that
+    will later be output in jsonData().  It allows for more advanced
+    configuration than the default path handling that JSTree currently allows.
+    For example, users may want to pass "attr" or some other valid jsTree options.
+
+    Example:
+      >>> import jstree
+      >>> node = jstree.Node('a', None)
+      >>> print node
+      Node({'text': 'a', 'children': MutableDictionaryObject({})})
+      >>> print node.jsonData()
+      {'text': 'a'}
+
+      >>> import jstree
+      >>> node = jstree.Node('a', 1)
+      >>> print node
+      Node({'text': 'a', 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 1}), 'id': 1})
+      >>> print node.jsonData()
+      {'text': 'a', 'id': 1, 'li_attr': {'id': 1}}
+
+      >>> import jstree
+      >>> node = jstree.Node('a', 5, icon="folder", state = {'opened': True})
+      >>> print node
+      Node({'text': 'a', 'id': 5, 'state': DictionaryObject({'opened': True}), 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 5}), 'icon': 'folder'})
+      >>> print node.jsonData()
+      {'text': 'a', 'state': {'opened': True}, 'id': 5, 'li_attr': {'id': 5}, 'icon': 'folder'}
+    """
+    super(Node, self).__init__()
+
+    children = kwargs.get('children', {})
+    if len(filter(lambda key: not isinstance(children[key], Node), children)):
+      raise TypeError(
+        "One or more children were not instances of '%s'" % Node.__name__)
+    if 'children' in kwargs:
+      del kwargs['children']
+    self._items['children'] = dictobj.MutableDictionaryObject(children)
+
+    if oid is not None:
+      li_attr = kwargs.get('li_attr', {})
+      li_attr['id'] = oid
+      kwargs['li_attr'] = li_attr
+      self._items['id'] = oid
+
+    self._items.update(dictobj.DictionaryObject(**kwargs))
+    self._items['text'] = path
+
+  def jsonData(self):
+    children = [self.children[k].jsonData() for k in sorted(self.children)]
+    output = {}
+    for k in self._items:
+      if 'children' == k:
+        continue
+      if isinstance(self._items[k], dictobj.DictionaryObject):
+        output[k] = self._items[k].asdict()
+      else:
+        output[k] = self._items[k]
+    if len(children):
+      output['children'] = children
+    return output
+
+
+class JSTree(dictobj.DictionaryObject):
+  """
+  An immutable dictionary-like object that converts a list of "paths"
+  into a tree structure suitable for jQuery's jsTree.
+  """
+
+  def __init__(self, paths, **kwargs):
+    """
+    Take a list of paths and put them into a tree.  Paths with the same prefix should
+    be at the same level in the tree.
+
+    kwargs may be standard jsTree options used at all levels in the tree.  These will be outputted
+    in the JSON.
+
+    Example (basic usage):
+      >>> import jstree
+      >>> paths = [jstree.Path("editor/2012-07/31/.classpath", 1), jstree.Path("editor/2012-07/31/.project", 2)]
+      >>> t1 = jstree.JSTree(paths)
+      >>> print t1.jsonData()
+      [{'text': 'editor/2012-07/31/.classpath', 'id': 1, 'li_attr': {'id': 1}}, {'text': 'editor/2012-07/31/.project', 'id': 2, 'li_attr': {'id': 2}}]
+    """
+    if len(filter(lambda p: not isinstance(p, Path), paths)):
+      raise TypeError(
+        "All paths must be instances of '%s'" % Path.__name__)
+
+    super(JSTree, self).__init__()
+
+    root = Node('', None, **kwargs)
+    for path in sorted(paths):
+      curr = root
+      subpaths = path.path.split(os.path.sep)
+      for i, subpath in enumerate(subpaths):
+        if subpath not in curr.children:
+          opt = copy.deepcopy(kwargs)
+          if len(subpaths) - 1 == i:
+            oid = path.id
+            opt.update(path.options) if path.options is not None else None
+          else:
+            oid = None
+          curr.children[subpath] = Node(subpath, oid, **opt)          
+          # oid = path.id if len(subpaths) - 1 == i else None
+          # curr.children[subpath] = Node(subpath, oid, **kwargs)
+        curr = curr.children[subpath]
+    self._items['_root'] = root
+
+  def pretty(self, root=None, depth=0, spacing=2):
+    """
+    Create a "pretty print" represenation of the tree with customized indentation at each
+    level of the tree.
+
+    Example:
+    >>> import jstree
+    >>> paths = [jstree.Path("editor/2012-07/31/.classpath", 1), jstree.Path("editor/2012-07/31/.project", 2)]
+    >>> print jstree.JSTree(paths).pretty()
+    /
+      editor/
+      2012-07/
+        31/
+        .classpath
+        .project
+    """
+    if root is None:
+      root = self._root
+    fmt = "%s%s/" if root.children else "%s%s"
+    s = fmt % (" " * depth * spacing, root.text)
+    for child in root.children:
+      child = root.children[child]
+      s += "\n%s" % self.pretty(child, depth + 1, spacing)
+    return s
+
+  def jsonData(self):
+    """
+    Returns a copy of the internal tree in a JSON-friendly format,
+    ready for consumption by jsTree.  The data is represented as a
+    list of dictionaries, each of which are our internal nodes.
+
+    Examples:
+    >>> import jstree
+    >>> paths = [jstree.Path("editor/2012-07/31/.classpath", 1), jstree.Path("editor/2012-07/31/.project", 2)]
+    >>> t = jstree.JSTree(paths)
+    >>> d = t.jsonData()
+    >>> print d
+    [{'data': 'editor', 'children': [{'data': '2012-07', 'children': [{'data': '31', 'children': [{'data': '.classpath', 'metadata': {'id': 1}}, {'data': '.project', 'metadata': {'id': 2}}]}]}]}]
+    >>> print d[0]['children'][0]['children'][0]['children'][1]
+    {'data': '.project', 'metadata': {'id': 2}}
+    >>> print d[0]['children'][0]['children'][0]['children'][1]['data']
+    .project
+    >>> print d[0]['children'][0]['children'][0]['children'][1]['metadata']['id']
+    2
+    """
+    return [self._root.children[k].jsonData() for k in sorted(self._root.children)]

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 lib/galaxy/webapps/galaxy/api/folder_contents.py
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -4,6 +4,7 @@
 from galaxy import web
 from galaxy import util
 from galaxy import exceptions
+from galaxy.managers import folders
 from galaxy.web import _future_expose_api as expose_api
 from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
 from sqlalchemy.orm.exc import MultipleResultsFound
@@ -19,6 +20,10 @@
     Class controls retrieval, creation and updating of folder contents.
     """
 
+    def __init__( self, app ):
+        super( FolderContentsController, self ).__init__( app )
+        self.folder_manager = folders.FolderManager()
+
     @expose_api_anonymous
     def index( self, trans, folder_id, **kwd ):
         """
@@ -46,32 +51,17 @@
         """
         is_admin = trans.user_is_admin()
         deleted = kwd.get( 'include_deleted', 'missing' )
+        current_user_roles = trans.get_current_user_roles()
         try:
             deleted = util.asbool( deleted )
         except ValueError:
             deleted = False
 
-        if ( len( folder_id ) == 17 and folder_id.startswith( 'F' ) ):
-            try:
-                decoded_folder_id = trans.security.decode_id( folder_id[ 1: ] )
-            except TypeError:
-                raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) )
-        else:
-            raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) )
-
-        try:
-            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one()
-        except MultipleResultsFound:
-            raise exceptions.InconsistentDatabase( 'Multiple folders with same id found.' )
-        except NoResultFound:
-            raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
-        except Exception:
-            raise exceptions.InternalServerError( 'Error loading from the database.' )
-
-        current_user_roles = trans.get_current_user_roles()
+        decoded_folder_id = self.folder_manager.cut_and_decode( trans, folder_id )
+        folder = self.folder_manager.get( trans, decoded_folder_id )
 
         # Special level of security on top of libraries.
-        if trans.app.security_agent.can_access_library( current_user_roles, folder.parent_library ):
+        if trans.app.security_agent.can_access_library( current_user_roles, folder.parent_library ) or is_admin:
             pass
         else:
             if trans.user:
@@ -80,29 +70,6 @@
                 log.warning( "SECURITY: Anonymous user is trying to load restricted folder with ID of %s" % ( decoded_folder_id ) )
             raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
 
-        # if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ):
-        #     log.debug('folder parent id:   ' + str(folder.parent_id))
-        #     if folder.parent_id is None:
-        #         try:
-        #             library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one()
-        #         except Exception:
-        #             raise exceptions.InternalServerError( 'Error loading from the database.' )
-        #         if trans.app.security_agent.library_is_unrestricted( library ):
-        #             pass
-        #         else:
-        #             if trans.user:
-        #                 log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) )
-        #             else:
-        #                 log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) )
-        #             raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
-            # else:
-            #     if trans.user:
-            #         log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) )
-            #     else:
-            #         log.debug('PARENT ID IS NOT NONE')
-            #         log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) )
-            #     raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
-
         folder_contents = []
         update_time = ''
         create_time = ''
@@ -161,9 +128,11 @@
 
         # Check whether user can modify the current folder
         can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, folder )
+        
         parent_library_id = None
         if folder.parent_library is not None:
             parent_library_id = trans.security.encode_id( folder.parent_library.id )
+
         metadata = dict( full_path=full_path,
                          can_add_library_item=can_add_library_item,
                          can_modify_folder=can_modify_folder,

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 lib/galaxy/webapps/galaxy/api/ftp_files.py
--- a/lib/galaxy/webapps/galaxy/api/ftp_files.py
+++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py
@@ -1,60 +1,127 @@
 """
-API operations on ftp files.
+API operations on remote files.
 """
-import logging
-from galaxy.web.base.controller import BaseAPIController, url_for
-from galaxy import web
-import os.path
 import os
 import time
+import hashlib
+from galaxy import web
+from galaxy import exceptions
+from galaxy.web import _future_expose_api as expose_api
+from galaxy.util import jstree
+from galaxy.web.base.controller import BaseAPIController, url_for
 from operator import itemgetter
 
+import logging
 log = logging.getLogger( __name__ )
 
 class FTPFilesAPIController( BaseAPIController ):
-    @web.expose_api
+
+    @expose_api
     def index( self, trans, **kwd ):
         """
         GET /api/ftp_files/
-        Displays local files.
+
+        Displays remote files.
+
+        :param  target:      target to load available datasets from, defaults to ftp
+            possible values: ftp, userdir
+        :type   target:      str
+
+        :param  format:      requested format of data, defaults to flat
+            possible values: flat, jstree, ajax
+
+        :returns:   list of available files
+        :rtype:     list
         """
-        
-        # look for ftp files
-        try:
-            # initialize response
-            response = []
-            
-            # identify ftp directory
+        target = kwd.get( 'target', None )
+        format = kwd.get( 'format', None )
+
+        if target == 'userdir':
+            user_login = trans.user.email
+            user_base_dir = trans.app.config.user_library_import_dir
+            if user_base_dir is None:
+                raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' )
+            full_import_dir = os.path.join( user_base_dir, user_login )
+            if full_import_dir is not None:
+                if format == 'jstree':
+                    disable = kwd.get( 'disable', 'folders')
+                    try:
+                        userdir_jstree = self.__create_jstree( full_import_dir, disable )
+                        response = userdir_jstree.jsonData()
+                    except Exception, exception:
+                        log.debug(str(exception))
+                        raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( full_import_dir ) )
+                elif format == 'ajax':
+                    raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' )
+                else:
+                    try:
+                        response = self.__load_all_filenames( full_import_dir )
+                    except Exception, exception:
+                        log.error( 'Could not get user import files: %s', str( exception ), exc_info=True )
+                        raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' )
+            else:
+                raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' )
+        else:
             user_ftp_base_dir = trans.app.config.ftp_upload_dir
             if user_ftp_base_dir is None:
-                return []
-        
-            # identify user sub directory
-            user_ftp_dir = None
-            if user_ftp_base_dir is not None and trans is not None and trans.user is not None:
+                raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from FTP directories.' )
+            try:
+                user_ftp_dir = None
                 identifier = trans.app.config.ftp_upload_dir_identifier
                 user_ftp_dir = os.path.join( user_ftp_base_dir, getattr(trans.user, identifier) )
-            if user_ftp_dir is None:
-                return []
+                if user_ftp_dir is not None:
+                    response = self.__load_all_filenames( user_ftp_dir )
+                else:
+                    raise exceptions.ConfigDoesNotAllowException( 'You do not have an FTP directory named as your login at this Galaxy instance.' )
+            except Exception, exception:
+                log.error( 'Could not get ftp files: %s', str( exception ), exc_info=True )
+                raise exceptions.InternalServerError( 'Could not get the files from your FTP folder.' )
+        return response
 
-            # read directory
-            if os.path.exists( user_ftp_dir ):
-                for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ):
-                    for filename in filenames:
-                        path = os.path.relpath( os.path.join( dirpath, filename ), user_ftp_dir )
-                        statinfo = os.lstat( os.path.join( dirpath, filename ) )
-                        response.append( dict(  path    = path,
-                                                size    = statinfo.st_size,
-                                                ctime   = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) )
-            
-                # sort by path
-                response = sorted(response, key=itemgetter("path"))
+    def __load_all_filenames( self, directory ):
+        """
+        Loads recursively all files within the given folder and its
+        subfolders and returns a flat list.
+        """
+        response = []
+        if os.path.exists( directory ):
+            for ( dirpath, dirnames, filenames ) in os.walk( directory ):
+                for filename in filenames:
+                    path = os.path.relpath( os.path.join( dirpath, filename ), directory )
+                    statinfo = os.lstat( os.path.join( dirpath, filename ) )
+                    response.append( dict(  path    = path,
+                                            size    = statinfo.st_size,
+                                            ctime   = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) )
+        else:
+            raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' )
+        # sort by path
+        response = sorted(response, key=itemgetter("path"))
+        return response
 
-            # return
-            return response
-        
-        except Exception, exception:
-            log.error( 'could not get ftp files: %s', str( exception ), exc_info=True )
-            trans.response.status = 500
-            return { 'error': str( exception ) }
+    def __create_jstree( self, directory, disable='folders' ):
+        """
+        Loads recursively all files and folders within the given folder
+        and its subfolders and returns jstree representation
+        of its structure.
+        """
+        userdir_jstree = None
+        jstree_paths = []
+        if os.path.exists( directory ):
+            for ( dirpath, dirnames, filenames ) in os.walk( directory ):
 
+                for dirname in dirnames:
+                    dir_path = os.path.relpath( os.path.join( dirpath, dirname ), directory )
+                    dir_path_hash = hashlib.sha1( dir_path ).hexdigest()
+                    disabled = True if disable == 'folders' else False
+                    jstree_paths.append( jstree.Path( dir_path, dir_path_hash, { 'type': 'folder', 'state': { 'disabled': disabled }, 'li_attr': { 'full_path': dir_path } } ) )
+
+                for filename in filenames:
+                    file_path = os.path.relpath( os.path.join( dirpath, filename ), directory )
+                    file_path_hash = hashlib.sha1( file_path ).hexdigest()
+                    disabled = True if disable == 'files' else False
+                    jstree_paths.append( jstree.Path( file_path, file_path_hash, { 'type': 'file', 'state': { 'disabled': disabled }, 'li_attr': { 'full_path': file_path } } ) )
+        else:
+            raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' )
+
+        userdir_jstree = jstree.JSTree( jstree_paths )
+        return userdir_jstree

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 lib/galaxy/webapps/galaxy/api/lda_datasets.py
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -1,5 +1,5 @@
 """
-API operations on the datasets from library.
+API operations on the library datasets.
 """
 import glob
 import operator
@@ -15,6 +15,7 @@
 from galaxy import web
 from galaxy import util
 from galaxy import exceptions
+from galaxy.managers import folders, roles
 from galaxy.exceptions import ObjectNotFound
 from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
 from galaxy.web import _future_expose_api as expose_api
@@ -24,6 +25,9 @@
 from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin
 from sqlalchemy.orm.exc import MultipleResultsFound
 from sqlalchemy.orm.exc import NoResultFound
+from galaxy.tools.actions import upload_common
+from galaxy.util.json import to_json_string, from_json_string
+
 
 import logging
 log = logging.getLogger( __name__ )
@@ -31,6 +35,11 @@
 
 class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
 
+    def __init__( self, app ):
+        super( LibraryDatasetsController, self ).__init__( app )
+        self.folder_manager = folders.FolderManager()
+        self.role_manager = roles.RoleManager()
+
     @expose_api_anonymous
     def show( self, trans, id, **kwd ):
         """
@@ -41,8 +50,8 @@
         :param  id:      the encoded id of the dataset to query
         :type   id:      an encoded id string
 
+        :returns:   detailed dataset information from base controller
         :rtype:     dictionary
-        :returns:   detailed dataset information from base controller
 
         .. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset`
         """
@@ -144,7 +153,6 @@
             raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to access permissions.' )
 
         scope = kwd.get( 'scope', None )
-
         if scope == 'current' or scope is None:
             return self._get_current_roles( trans, library_dataset )
 
@@ -394,6 +402,104 @@
         rval[ 'folder_id' ] = 'F' + rval[ 'folder_id' ]
         return rval
 
+    @expose_api
+    def load( self, trans, **kwd ):
+        """
+        Load dataset from the given source into the library.
+
+        :param  encoded_folder_id:      the encoded id of the folder to import dataset to
+        :type   encoded_folder_id:      an encoded id string
+        :param  source:                 source of the dataset to be loaded
+        :type   source:                 str
+        :param  link_data:              flag whether to link the dataset to data or copy it to Galaxy
+        :type   link_data:              bool
+        :param  preserve_dirs:          flag whether to preserver directory structure when importing dir
+        :type   preserve_dirs:          bool
+        """
+
+        kwd[ 'space_to_tab' ] = 'False'
+        kwd[ 'to_posix_lines' ] = 'True'
+        kwd[ 'dbkey' ] = '?'
+        kwd[ 'file_type' ] = 'auto'
+
+        kwd[' link_data_only' ] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
+        encoded_folder_id = kwd.get( 'encoded_folder_id', None )
+        if encoded_folder_id is not None:
+            folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id )
+        else:
+            raise exceptions.RequestParameterMissingException( 'The required atribute encoded_folder_id is missing.' )
+        path = kwd.get( 'path', None)
+        if path is None:
+            raise exceptions.RequestParameterMissingException( 'The required atribute path is missing.' )
+        folder = self.folder_manager.get( trans, folder_id )
+        link_data = util.string_as_bool( kwd.get( 'link_data', False ) )
+
+        source = kwd.get( 'source', None )
+        if source not in [ 'userdir_file', 'userdir_folder' ]:
+            raise exceptions.RequestParameterMissingException( 'You have to specify "source" parameter. Possible values are "userdir_file" and "userdir_folder". ')
+
+        user_login = trans.user.email
+        user_base_dir = trans.app.config.user_library_import_dir
+        if user_base_dir is None:
+            raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' )
+        full_dir = os.path.join( user_base_dir, user_login )
+        # path_to_root_import_folder = None
+        if not path.lower().startswith( full_dir.lower() ):
+            # path_to_root_import_folder = path
+            path = os.path.join( full_dir, path )
+        if not os.path.exists( path ):
+            raise exceptions.RequestParameterInvalidException( 'Given path does not exist on the host.' )
+        if not self.folder_manager.can_add_item( trans, folder ):
+            raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to add items to the given folder.' )
+
+        # Set up the traditional tool state/params
+        tool_id = 'upload1'
+        tool = trans.app.toolbox.get_tool( tool_id )
+        state = tool.new_state( trans )
+        errors = tool.update_state( trans, tool.inputs_by_page[ 0 ], state.inputs, kwd )
+        tool_params = state.inputs
+        dataset_upload_inputs = []
+        for input_name, input in tool.inputs.iteritems():
+            if input.type == "upload_dataset":
+                dataset_upload_inputs.append( input )
+        library_bunch = upload_common.handle_library_params( trans, {}, trans.security.encode_id( folder.id ) )
+        abspath_datasets = []
+        kwd[ 'filesystem_paths' ] = path
+        params = util.Params( kwd )
+        # file only
+        if source == "userdir_file":
+            file = os.path.abspath( path )
+            abspath_datasets.append( trans.webapp.controllers[ 'library_common' ].make_library_uploaded_dataset(
+                trans, 'api', params, os.path.basename( file ), file, 'server_dir', library_bunch ) )
+        # whole folder
+        if source == "userdir_folder":
+            # import_folder_root = [next(part for part in path.split(os.path.sep) if part) for path in [os.path.splitdrive(path_to_root_import_folder)[1]]]
+            # new_folder = self.folder_manager.create( trans, folder_id, import_folder_root[0] )
+
+            uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( 
+                trans, 'api', params, library_bunch, 200, '' )
+
+            uploaded_datasets = uploaded_datasets_bunch[0]
+            if uploaded_datasets is None:
+                #  TODO no files found - only create folders
+                return False
+
+            for ud in uploaded_datasets:
+                ud.path = os.path.abspath( ud.path )
+                abspath_datasets.append( ud )
+
+        json_file_path = upload_common.create_paramfile( trans, abspath_datasets )
+        data_list = [ ud.data for ud in abspath_datasets ]
+        job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=folder )
+        # HACK: Prevent outputs_to_working_directory from overwriting inputs when "linking"
+        job.add_parameter( 'link_data_only', to_json_string( kwd.get( 'link_data_only', 'copy_files' ) ) )
+        job.add_parameter( 'uuid', to_json_string( kwd.get( 'uuid', None ) ) )
+        trans.sa_session.add( job )
+        trans.sa_session.flush()
+        job_dict = job.to_dict()
+        job_dict[ 'id' ] = trans.security.encode_id( job_dict[ 'id' ] )
+        return job_dict
+
     @web.expose
     def download( self, trans, format, **kwd ):
         """

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -258,6 +258,12 @@
                            action='show',
                            conditions=dict( method=[ "GET" ] ) )
 
+    webapp.mapper.connect( 'load_ld',
+                           '/api/libraries/datasets/',
+                           controller='lda_datasets',
+                           action='load',
+                           conditions=dict( method=[ "POST" ] ) )
+
     webapp.mapper.connect( 'show_version_of_ld_item',
                            '/api/libraries/datasets/:encoded_dataset_id/versions/:encoded_ldda_id',
                            controller='lda_datasets',

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 static/images/jstree/32px.png
Binary file static/images/jstree/32px.png has changed

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 static/images/jstree/40px.png
Binary file static/images/jstree/40px.png has changed

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 static/images/jstree/throbber.gif
Binary file static/images/jstree/throbber.gif has changed

diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r cadad49537de2edd2128be108d0d631f35722ab5 static/scripts/galaxy.library.js
--- a/static/scripts/galaxy.library.js
+++ b/static/scripts/galaxy.library.js
@@ -47,7 +47,8 @@
     "folders/:folder_id/datasets/:dataset_id"                       : "dataset_detail",
     "folders/:folder_id/datasets/:dataset_id/permissions"           : "dataset_permissions",
     "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id"     : "dataset_version",
-    "folders/:folder_id/download/:format"                           : "download"
+    "folders/:folder_id/download/:format"                           : "download",
+    "folders/:folder_id/import/:source"                             : "import_datasets"
   },
 
   back: function() {
@@ -147,6 +148,15 @@
           }
           Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
        });
+       this.library_router.on('route:import_datasets', function(folder_id, source){
+          if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){
+            Galaxy.libraries.folderToolbarView.showImportModal({source:source});
+          } else {
+            Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id});
+            Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id});
+            Galaxy.libraries.folderToolbarView.showImportModal({source: source});
+          }
+       });
 
     Backbone.history.start({pushState: false});
     }

This diff is so big that we needed to truncate the remainder.

https://bitbucket.org/galaxy/galaxy-central/commits/ecf83c3a2d03/
Changeset:   ecf83c3a2d03
User:        martenson
Date:        2014-09-08 18:45:37+00:00
Summary:     adding compressed version of jstree jquery plugin
Affected #:  1 file

diff -r cadad49537de2edd2128be108d0d631f35722ab5 -r ecf83c3a2d0383c74e30dca41b602854326c7ee7 static/scripts/packed/libs/jquery/jstree.js
--- /dev/null
+++ b/static/scripts/packed/libs/jquery/jstree.js
@@ -0,0 +1,60 @@
+(function(a){if(typeof define==="function"&&define.amd){}else{if(typeof exports==="object"){a(require("jquery"))}else{a(jQuery)}}}(function(i,e){
+/*
+ * jsTree 3.0.3
+ * http://jstree.com/
+ *
+ * Copyright (c) 2014 Ivan Bozhanov (http://vakata.com)
+ *
+ * Licensed same as jquery - under the terms of the MIT License
+ *   http://www.opensource.org/licenses/mit-license.php
+ */
+/*
+ * if using jslint please allow for the jQuery global and use following options: 
+ * jslint: browser: true, ass: true, bitwise: true, continue: true, nomen: true, plusplus: true, regexp: true, unparam: true, todo: true, white: true
+ */
+if(i.jstree){return}var c=0,d=false,k=false,j=false,m=[],a=i("script:last").attr("src"),l=document,o=l.createElement("LI"),g,f;o.setAttribute("role","treeitem");g=l.createElement("I");g.className="jstree-icon jstree-ocl";o.appendChild(g);g=l.createElement("A");g.className="jstree-anchor";g.setAttribute("href","#");f=l.createElement("I");f.className="jstree-icon jstree-themeicon";g.appendChild(f);o.appendChild(g);g=f=null;i.jstree={version:"3.0.3",defaults:{plugins:[]},plugins:{},path:a&&a.indexOf("/")!==-1?a.replace(/\/[^\/]+$/,""):"",idregex:/[\\:&!^|()\[\]<>@*'+~#";.,=\- \/${}%]/g};i.jstree.create=function(s,p){var r=new i.jstree.core(++c),q=p;p=i.extend(true,{},i.jstree.defaults,p);if(q&&q.plugins){p.plugins=q.plugins}i.each(p.plugins,function(u,t){if(u!=="core"){r=r.plugin(t,p[t])}});r.init(s,p);return r};i.jstree.core=function(p){this._id=p;this._cnt=0;this._wrk=null;this._data={core:{themes:{name:false,dots:false,icons:false},selected:[],last_error:{},working:false,worker_queue:[]}}};i.jstree.reference=function(r){var p=null,q=null;if(r&&r.id){r=r.id}if(!q||!q.length){try{q=i(r)}catch(s){}}if(!q||!q.length){try{q=i("#"+r.replace(i.jstree.idregex,"\\$&"))}catch(s){}}if(q&&q.length&&(q=q.closest(".jstree")).length&&(q=q.data("jstree"))){p=q}else{i(".jstree").each(function(){var t=i(this).data("jstree");if(t&&t._model.data[r]){p=t;return false}})}return p};i.fn.jstree=function(q){var s=(typeof q==="string"),r=Array.prototype.slice.call(arguments,1),p=null;this.each(function(){var t=i.jstree.reference(this),u=s&&t?t[q]:null;p=s&&u?u.apply(t,r):null;if(!t&&!s&&(q===e||i.isPlainObject(q))){i(this).data("jstree",new i.jstree.create(this,q))}if((t&&!s)||q===true){p=t||false}if(p!==null&&p!==e){return false}});return 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jstree-"+this._id);this.settings=p;this.element.bind("destroyed",i.proxy(this.teardown,this));this._data.core.ready=false;this._data.core.loaded=false;this._data.core.rtl=(this.element.css("direction")==="rtl");this.element[this._data.core.rtl?"addClass":"removeClass"]("jstree-rtl");this.element.attr("role","tree");this.bind();this.trigger("init");this._data.core.original_container_html=this.element.find(" > ul > li").clone(true);this._data.core.original_container_html.find("li").addBack().contents().filter(function(){return this.nodeType===3&&(!this.nodeValue||/^\s+$/.test(this.nodeValue))}).remove();this.element.html("<ul class='jstree-container-ul jstree-children'><li class='jstree-initial-node jstree-loading jstree-leaf jstree-last'><i class='jstree-icon jstree-ocl'></i><a class='jstree-anchor' href='#'><i class='jstree-icon jstree-themeicon-hidden'></i>"+this.get_string("Loading 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39:p.preventDefault();if(this.is_closed(p.currentTarget)){this.open_node(p.currentTarget,function(r){this.get_node(r,true).children(".jstree-anchor").focus()})}else{q=this.get_next_dom(p.currentTarget);if(q&&q.length){q.children(".jstree-anchor").focus()}}break;case 40:p.preventDefault();q=this.get_next_dom(p.currentTarget);if(q&&q.length){q.children(".jstree-anchor").focus()}break;case 46:p.preventDefault();q=this.get_node(p.currentTarget);if(q&&q.id&&q.id!=="#"){q=this.is_selected(q)?this.get_selected():q}break;case 113:p.preventDefault();q=this.get_node(p.currentTarget);
+/*
+								if(o && o.id && o.id !== '#') {
+									// this.edit(o);
+								}
+								*/
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v.data.jstree){if(v.data.jstree.hasOwnProperty(w)){v.state[w]=v.data.jstree[w]}}}u=y.children("a").children(".jstree-themeicon");if(u.length){v.icon=u.hasClass("jstree-themeicon-hidden")?false:u.attr("rel")}if(v.state.icon){v.icon=v.state.icon}u=y.children("ul").children("li");do{t="j"+this._id+"_"+(++this._cnt)}while(s[t]);v.id=v.li_attr.id?v.li_attr.id.toString():t;if(u.length){u.each(i.proxy(function(A,p){z=this._parse_model_from_html(i(p),v.id,q);x=this._model.data[z];v.children.push(z);if(x.children_d.length){v.children_d=v.children_d.concat(x.children_d)}},this));v.children_d=v.children_d.concat(v.children)}else{if(y.hasClass("jstree-closed")){v.state.loaded=false}}if(v.li_attr["class"]){v.li_attr["class"]=v.li_attr["class"].replace("jstree-closed","").replace("jstree-open","")}if(v.a_attr["class"]){v.a_attr["class"]=v.a_attr["class"].replace("jstree-clicked","").replace("jstree-disabled","")}s[v.id]=v;if(v.state.selected){this._data.core.selected.push(v.id)}return v.id},_parse_model_from_flat_json:function(y,r,q){if(!q){q=[]}else{q=q.concat()}if(r){q.unshift(r)}var t=y.id.toString(),s=this._model.data,A=this._model.default_state,w,u,z,x,v={id:t,text:y.text||"",icon:y.icon!==e?y.icon:true,parent:r,parents:q,children:y.children||[],children_d:y.children_d||[],data:y.data,state:{},li_attr:{id:false},a_attr:{href:"#"},original:false};for(w in A){if(A.hasOwnProperty(w)){v.state[w]=A[w]}}if(y&&y.data&&y.data.jstree&&y.data.jstree.icon){v.icon=y.data.jstree.icon}if(y&&y.data){v.data=y.data;if(y.data.jstree){for(w in y.data.jstree){if(y.data.jstree.hasOwnProperty(w)){v.state[w]=y.data.jstree[w]}}}}if(y&&typeof y.state==="object"){for(w in y.state){if(y.state.hasOwnProperty(w)){v.state[w]=y.state[w]}}}if(y&&typeof y.li_attr==="object"){for(w in y.li_attr){if(y.li_attr.hasOwnProperty(w)){v.li_attr[w]=y.li_attr[w]}}}if(!v.li_attr.id){v.li_attr.id=t}if(y&&typeof y.a_attr==="object"){for(w in y.a_attr){if(y.a_attr.hasOwnProperty(w)){v.a_attr[w]=y.a_attr[w]}}}if(y&&y.children&&y.children===true){v.state.loaded=false;v.children=[];v.children_d=[]}s[v.id]=v;for(w=0,u=v.children.length;w<u;w++){z=this._parse_model_from_flat_json(s[v.children[w]],v.id,q);x=s[z];v.children_d.push(z);if(x.children_d.length){v.children_d=v.children_d.concat(x.children_d)}}delete y.data;delete y.children;s[v.id].original=y;if(v.state.selected){this._data.core.selected.push(v.id)}return v.id},_parse_model_from_json:function(y,r,q){if(!q){q=[]}else{q=q.concat()}if(r){q.unshift(r)}var t=false,w,u,z,x,s=this._model.data,A=this._model.default_state,v;do{t="j"+this._id+"_"+(++this._cnt)}while(s[t]);v={id:false,text:typeof y==="string"?y:"",icon:typeof y==="object"&&y.icon!==e?y.icon:true,parent:r,parents:q,children:[],children_d:[],data:null,state:{},li_attr:{id:false},a_attr:{href:"#"},original:false};for(w in A){if(A.hasOwnProperty(w)){v.state[w]=A[w]}}if(y&&y.id){v.id=y.id.toString()}if(y&&y.text){v.text=y.text}if(y&&y.data&&y.data.jstree&&y.data.jstree.icon){v.icon=y.data.jstree.icon}if(y&&y.data){v.data=y.data;if(y.data.jstree){for(w in y.data.jstree){if(y.data.jstree.hasOwnProperty(w)){v.state[w]=y.data.jstree[w]}}}}if(y&&typeof y.state==="object"){for(w in y.state){if(y.state.hasOwnProperty(w)){v.state[w]=y.state[w]}}}if(y&&typeof y.li_attr==="object"){for(w in y.li_attr){if(y.li_attr.hasOwnProperty(w)){v.li_attr[w]=y.li_attr[w]}}}if(v.li_attr.id&&!v.id){v.id=v.li_attr.id.toString()}if(!v.id){v.id=t}if(!v.li_attr.id){v.li_attr.id=v.id}if(y&&typeof y.a_attr==="object"){for(w in y.a_attr){if(y.a_attr.hasOwnProperty(w)){v.a_attr[w]=y.a_attr[w]}}}if(y&&y.children&&y.children.length){for(w=0,u=y.children.length;w<u;w++){z=this._parse_model_from_json(y.children[w],v.id,q);x=s[z];v.children.push(z);if(x.children_d.length){v.children_d=v.children_d.concat(x.children_d)}}v.children_d=v.children_d.concat(v.children)}if(y&&y.children&&y.children===true){v.state.loaded=false;v.children=[];v.children_d=[]}delete y.data;delete y.children;v.original=y;s[v.id]=v;if(v.state.selected){this._data.core.selected.push(v.id)}return v.id},_redraw:function(){var p=this._model.force_full_redraw?this._model.data["#"].children.concat([]):this._model.changed.concat([]),t=document.createElement("UL"),s,r,q;for(r=0,q=p.length;r<q;r++){s=this.redraw_node(p[r],true,this._model.force_full_redraw);if(s&&this._model.force_full_redraw){t.appendChild(s)}}if(this._model.force_full_redraw){t.className=this.get_container_ul()[0].className;this.element.empty().append(t)}this._model.force_full_redraw=false;this._model.changed=[];this.trigger("redraw",{nodes:p})},redraw:function(p){if(p){this._model.force_full_redraw=true}this._redraw()},redraw_node:function(t,E,D){var x=this.get_node(t),B=false,p=false,q=false,y=false,v=false,u=false,C="",A=document,r=this._model.data,z=false,F=false,w=null;if(!x){return false}if(x.id==="#"){return this.redraw(true)}E=E||x.children.length===0;t=!document.querySelector?document.getElementById(x.id):this.element[0].querySelector("#"+("0123456789".indexOf(x.id[0])!==-1?"\\3"+x.id[0]+" "+x.id.substr(1).replace(i.jstree.idregex,"\\$&"):x.id.replace(i.jstree.idregex,"\\$&")));if(!t){E=true;if(!D){B=x.parent!=="#"?i("#"+x.parent.replace(i.jstree.idregex,"\\$&"),this.element)[0]:null;if(B!==null&&(!B||!r[x.parent].state.opened)){return false}p=i.inArray(x.id,B===null?r["#"].children:r[x.parent].children)}}else{t=i(t);if(!D){B=t.parent().parent()[0];if(B===this.element[0]){B=null}p=t.index()}if(!E&&x.children.length&&!t.children(".jstree-children").length){E=true}if(!E){q=t.children(".jstree-children")[0]}F=t.attr("aria-selected");z=t.children(".jstree-anchor")[0]===document.activeElement;t.remove()}t=o.cloneNode(true);C="jstree-node ";for(y in x.li_attr){if(x.li_attr.hasOwnProperty(y)){if(y==="id"){continue}if(y!=="class"){t.setAttribute(y,x.li_attr[y])}else{C+=x.li_attr[y]}}}if(F&&F!=="false"){t.setAttribute("aria-selected",true)}if(x.state.loaded&&!x.children.length){C+=" jstree-leaf"}else{C+=x.state.opened&&x.state.loaded?" jstree-open":" jstree-closed";t.setAttribute("aria-expanded",(x.state.opened&&x.state.loaded))}if(x.parent!==null&&r[x.parent].children[r[x.parent].children.length-1]===x.id){C+=" jstree-last"}t.id=x.id;t.className=C;C=(x.state.selected?" jstree-clicked":"")+(x.state.disabled?" jstree-disabled":"");for(v in x.a_attr){if(x.a_attr.hasOwnProperty(v)){if(v==="href"&&x.a_attr[v]==="#"){continue}if(v!=="class"){t.childNodes[1].setAttribute(v,x.a_attr[v])}else{C+=" "+x.a_attr[v]}}}if(C.length){t.childNodes[1].className="jstree-anchor "+C}if((x.icon&&x.icon!==true)||x.icon===false){if(x.icon===false){t.childNodes[1].childNodes[0].className+=" jstree-themeicon-hidden"}else{if(x.icon.indexOf("/")===-1&&x.icon.indexOf(".")===-1){t.childNodes[1].childNodes[0].className+=" "+x.icon+" jstree-themeicon-custom"}else{t.childNodes[1].childNodes[0].style.backgroundImage="url("+x.icon+")";t.childNodes[1].childNodes[0].style.backgroundPosition="center center";t.childNodes[1].childNodes[0].style.backgroundSize="auto";t.childNodes[1].childNodes[0].className+=" jstree-themeicon-custom"}}}if(this.settings.core.force_text){t.childNodes[1].appendChild(A.createTextNode(x.text))}else{t.childNodes[1].innerHTML+=x.text}if(E&&x.children.length&&x.state.opened&&x.state.loaded){u=A.createElement("UL");u.setAttribute("role","group");u.className="jstree-children";for(y=0,v=x.children.length;y<v;y++){u.appendChild(this.redraw_node(x.children[y],E,true))}t.appendChild(u)}if(q){t.appendChild(q)}if(!D){if(!B){B=this.element[0]}for(y=0,v=B.childNodes.length;y<v;y++){if(B.childNodes[y]&&B.childNodes[y].className&&B.childNodes[y].className.indexOf("jstree-children")!==-1){w=B.childNodes[y];break}}if(!w){w=A.createElement("UL");w.setAttribute("role","group");w.className="jstree-children";B.appendChild(w)}B=w;if(p<B.childNodes.length){B.insertBefore(t,B.childNodes[p])}else{B.appendChild(t)}if(z){t.childNodes[1].focus()}}if(x.state.opened&&!x.state.loaded){x.state.opened=false;setTimeout(i.proxy(function(){this.open_node(x.id,false,0)},this),0)}return t},open_node:function(u,w,s){var r,q,v,p;if(i.isArray(u)){u=u.slice();for(r=0,q=u.length;r<q;r++){this.open_node(u[r],w,s)}return true}u=this.get_node(u);if(!u||u.id==="#"){return false}s=s===e?this.settings.core.animation:s;if(!this.is_closed(u)){if(w){w.call(this,u,false)}return false}if(!this.is_loaded(u)){if(this.is_loading(u)){return setTimeout(i.proxy(function(){this.open_node(u,w,s)},this),500)}this.load_node(u,function(x,t){return t?this.open_node(x,w,s):(w?w.call(this,x,false):false)})}else{v=this.get_node(u,true);p=this;if(v.length){if(u.children.length&&!this._firstChild(v.children(".jstree-children")[0])){u.state.opened=true;this.redraw_node(u,true);v=this.get_node(u,true)}if(!s){this.trigger("before_open",{node:u});v[0].className=v[0].className.replace("jstree-closed","jstree-open");v[0].setAttribute("aria-expanded",true)}else{this.trigger("before_open",{node:u});v.children(".jstree-children").css("display","none").end().removeClass("jstree-closed").addClass("jstree-open").attr("aria-expanded",true).children(".jstree-children").stop(true,true).slideDown(s,function(){this.style.display="";p.trigger("after_open",{node:u})})}}u.state.opened=true;if(w){w.call(this,u,true)}if(!v.length){this.trigger("before_open",{node:u})}this.trigger("open_node",{node:u});if(!s||!v.length){this.trigger("after_open",{node:u})}}},_open_to:function(t){t=this.get_node(t);if(!t||t.id==="#"){return false}var r,q,s=t.parents;for(r=0,q=s.length;r<q;r+=1){if(r!=="#"){this.open_node(s[r],false,0)}}return i("#"+t.id.replace(i.jstree.idregex,"\\$&"),this.element)},close_node:function(u,s){var r,q,p,v;if(i.isArray(u)){u=u.slice();for(r=0,q=u.length;r<q;r++){this.close_node(u[r],s)}return true}u=this.get_node(u);if(!u||u.id==="#"){return false}if(this.is_closed(u)){return false}s=s===e?this.settings.core.animation:s;p=this;v=this.get_node(u,true);if(v.length){if(!s){v[0].className=v[0].className.replace("jstree-open","jstree-closed");v.attr("aria-expanded",false).children(".jstree-children").remove()}else{v.children(".jstree-children").attr("style","display:block !important").end().removeClass("jstree-open").addClass("jstree-closed").attr("aria-expanded",false).children(".jstree-children").stop(true,true).slideUp(s,function(){this.style.display="";v.children(".jstree-children").remove();p.trigger("after_close",{node:u})})}}u.state.opened=false;this.trigger("close_node",{node:u});if(!s||!v.length){this.trigger("after_close",{node:u})}},toggle_node:function(r){var q,p;if(i.isArray(r)){r=r.slice();for(q=0,p=r.length;q<p;q++){this.toggle_node(r[q])}return true}if(this.is_closed(r)){return this.open_node(r)}if(this.is_open(r)){return this.close_node(r)}},open_all:function(t,s,p){if(!t){t="#"}t=this.get_node(t);if(!t){return false}var u=t.id==="#"?this.get_container_ul():this.get_node(t,true),r,q,v;if(!u.length){for(r=0,q=t.children_d.length;r<q;r++){if(this.is_closed(this._model.data[t.children_d[r]])){this._model.data[t.children_d[r]].state.opened=true}}return this.trigger("open_all",{node:t})}p=p||u;v=this;u=this.is_closed(t)?u.find(".jstree-closed").addBack():u.find(".jstree-closed");u.each(function(){v.open_node(this,function(x,w){if(w&&this.is_parent(x)){this.open_all(x,s,p)}},s||0)});if(p.find(".jstree-closed").length===0){this.trigger("open_all",{node:this.get_node(p)})}},close_all:function(s,r){if(!s){s="#"}s=this.get_node(s);if(!s){return false}var t=s.id==="#"?this.get_container_ul():this.get_node(s,true),u=this,q,p;if(!t.length){for(q=0,p=s.children_d.length;q<p;q++){this._model.data[s.children_d[q]].state.opened=false}return this.trigger("close_all",{node:s})}t=this.is_open(s)?t.find(".jstree-open").addBack():t.find(".jstree-open");i(t.get().reverse()).each(function(){u.close_node(this,r||0)});this.trigger("close_all",{node:s})},is_disabled:function(p){p=this.get_node(p);return p&&p.state&&p.state.disabled},enable_node:function(r){var q,p;if(i.isArray(r)){r=r.slice();for(q=0,p=r.length;q<p;q++){this.enable_node(r[q])}return true}r=this.get_node(r);if(!r||r.id==="#"){return false}r.state.disabled=false;this.get_node(r,true).children(".jstree-anchor").removeClass("jstree-disabled");this.trigger("enable_node",{node:r})},disable_node:function(r){var q,p;if(i.isArray(r)){r=r.slice();for(q=0,p=r.length;q<p;q++){this.disable_node(r[q])}return true}r=this.get_node(r);if(!r||r.id==="#"){return false}r.state.disabled=true;this.get_node(r,true).children(".jstree-anchor").addClass("jstree-disabled");this.trigger("disable_node",{node:r})},activate_node:function(v,u){if(this.is_disabled(v)){return false}this._data.core.last_clicked=this._data.core.last_clicked&&this._data.core.last_clicked.id!==e?this.get_node(this._data.core.last_clicked.id):null;if(this._data.core.last_clicked&&!this._data.core.last_clicked.state.selected){this._data.core.last_clicked=null}if(!this._data.core.last_clicked&&this._data.core.selected.length){this._data.core.last_clicked=this.get_node(this._data.core.selected[this._data.core.selected.length-1])}if(!this.settings.core.multiple||(!u.metaKey&&!u.ctrlKey&&!u.shiftKey)||(u.shiftKey&&(!this._data.core.last_clicked||!this.get_parent(v)||this.get_parent(v)!==this._data.core.last_clicked.parent))){if(!this.settings.core.multiple&&(u.metaKey||u.ctrlKey||u.shiftKey)&&this.is_selected(v)){this.deselect_node(v,false,u)}else{this.deselect_all(true);this.select_node(v,false,false,u);this._data.core.last_clicked=this.get_node(v)}}else{if(u.shiftKey){var w=this.get_node(v).id,q=this._data.core.last_clicked.id,t=this.get_node(this._data.core.last_clicked.parent).children,x=false,s,r;for(s=0,r=t.length;s<r;s+=1){if(t[s]===w){x=!x}if(t[s]===q){x=!x}if(x||t[s]===w||t[s]===q){this.select_node(t[s],false,false,u)}else{this.deselect_node(t[s],false,u)}}}else{if(!this.is_selected(v)){this.select_node(v,false,false,u)}else{this.deselect_node(v,false,u)}}}this.trigger("activate_node",{node:this.get_node(v)})},hover_node:function(q){q=this.get_node(q,true);if(!q||!q.length||q.children(".jstree-hovered").length){return false}var r=this.element.find(".jstree-hovered"),p=this.element;if(r&&r.length){this.dehover_node(r)}q.children(".jstree-anchor").addClass("jstree-hovered");this.trigger("hover_node",{node:this.get_node(q)});setTimeout(function(){p.attr("aria-activedescendant",q[0].id);q.attr("aria-selected",true)},0)},dehover_node:function(p){p=this.get_node(p,true);if(!p||!p.length||!p.children(".jstree-hovered").length){return false}p.attr("aria-selected",false).children(".jstree-anchor").removeClass("jstree-hovered");this.trigger("dehover_node",{node:this.get_node(p)})},select_node:function(u,w,p,t){var v,s,q,r;if(i.isArray(u)){u=u.slice();for(s=0,q=u.length;s<q;s++){this.select_node(u[s],w,p,t)}return true}u=this.get_node(u);if(!u||u.id==="#"){return false}v=this.get_node(u,true);if(!u.state.selected){u.state.selected=true;this._data.core.selected.push(u.id);if(!p){v=this._open_to(u)}if(v&&v.length){v.children(".jstree-anchor").addClass("jstree-clicked")}this.trigger("select_node",{node:u,selected:this._data.core.selected,event:t});if(!w){this.trigger("changed",{action:"select_node",node:u,selected:this._data.core.selected,event:t})}}},deselect_node:function(s,u,r){var q,p,t;if(i.isArray(s)){s=s.slice();for(q=0,p=s.length;q<p;q++){this.deselect_node(s[q],u,r)}return true}s=this.get_node(s);if(!s||s.id==="#"){return false}t=this.get_node(s,true);if(s.state.selected){s.state.selected=false;this._data.core.selected=i.vakata.array_remove_item(this._data.core.selected,s.id);if(t.length){t.children(".jstree-anchor").removeClass("jstree-clicked")}this.trigger("deselect_node",{node:s,selected:this._data.core.selected,event:r});if(!u){this.trigger("changed",{action:"deselect_node",node:s,selected:this._data.core.selected,event:r})}}},select_all:function(s){var r=this._data.core.selected.concat([]),q,p;this._data.core.selected=this._model.data["#"].children_d.concat();for(q=0,p=this._data.core.selected.length;q<p;q++){if(this._model.data[this._data.core.selected[q]]){this._model.data[this._data.core.selected[q]].state.selected=true}}this.redraw(true);this.trigger("select_all",{selected:this._data.core.selected});if(!s){this.trigger("changed",{action:"select_all",selected:this._data.core.selected,old_selection:r})}},deselect_all:function(s){var r=this._data.core.selected.concat([]),q,p;for(q=0,p=this._data.core.selected.length;q<p;q++){if(this._model.data[this._data.core.selected[q]]){this._model.data[this._data.core.selected[q]].state.selected=false}}this._data.core.selected=[];this.element.find(".jstree-clicked").removeClass("jstree-clicked");this.trigger("deselect_all",{selected:this._data.core.selected,node:r});if(!s){this.trigger("changed",{action:"deselect_all",selected:this._data.core.selected,old_selection:r})}},is_selected:function(p){p=this.get_node(p);if(!p||p.id==="#"){return false}return p.state.selected},get_selected:function(p){return p?i.map(this._data.core.selected,i.proxy(function(q){return this.get_node(q)},this)):this._data.core.selected.slice()},get_top_selected:function(u){var t=this.get_selected(true),v={},s,r,q,p;for(s=0,r=t.length;s<r;s++){v[t[s].id]=t[s]}for(s=0,r=t.length;s<r;s++){for(q=0,p=t[s].children_d.length;q<p;q++){if(v[t[s].children_d[q]]){delete v[t[s].children_d[q]]}}}t=[];for(s in v){if(v.hasOwnProperty(s)){t.push(s)}}return u?i.map(t,i.proxy(function(w){return this.get_node(w)},this)):t},get_bottom_selected:function(s){var r=this.get_selected(true),t=[],q,p;for(q=0,p=r.length;q<p;q++){if(!r[q].children.length){t.push(r[q].id)}}return s?i.map(t,i.proxy(function(u){return this.get_node(u)},this)):t},get_state:function(){var q={core:{open:[],scroll:{left:this.element.scrollLeft(),top:this.element.scrollTop()},
+/*
+					'themes' : {
+						'name' : this.get_theme(),
+						'icons' : this._data.core.themes.icons,
+						'dots' : this._data.core.themes.dots
+					},
+					*/
+selected:[]}},p;for(p in this._model.data){if(this._model.data.hasOwnProperty(p)){if(p!=="#"){if(this._model.data[p].state.opened){q.core.open.push(p)}if(this._model.data[p].state.selected){q.core.selected.push(p)}}}}return q},set_state:function(r,v){if(r){if(r.core){var q,u,p,s;if(r.core.open){if(!i.isArray(r.core.open)){delete r.core.open;this.set_state(r,v);return false}q=true;u=false;p=this;i.each(r.core.open.concat([]),function(w,t){u=p.get_node(t);if(u){if(p.is_loaded(t)){if(p.is_closed(t)){p.open_node(t,false,0)}if(r&&r.core&&r.core.open){i.vakata.array_remove_item(r.core.open,t)}}else{if(!p.is_loading(t)){p.open_node(t,i.proxy(function(y,x){if(!x&&r&&r.core&&r.core.open){i.vakata.array_remove_item(r.core.open,y.id)}this.set_state(r,v)},p),0)}q=false}}});if(q){delete r.core.open;this.set_state(r,v)}return false}if(r.core.scroll){if(r.core.scroll&&r.core.scroll.left!==e){this.element.scrollLeft(r.core.scroll.left)}if(r.core.scroll&&r.core.scroll.top!==e){this.element.scrollTop(r.core.scroll.top)}delete r.core.scroll;this.set_state(r,v);return false;
+/*
+					if(state.core.themes) {
+						if(state.core.themes.name) {
+							this.set_theme(state.core.themes.name);
+						}
+						if(typeof state.core.themes.dots !== 'undefined') {
+							this[ state.core.themes.dots ? "show_dots" : "hide_dots" ]();
+						}
+						if(typeof state.core.themes.icons !== 'undefined') {
+							this[ state.core.themes.icons ? "show_icons" : "hide_icons" ]();
+						}
+						delete state.core.themes;
+						delete state.core.open;
+						this.set_state(state, callback);
+						return false;
+					}
+					*/
+}if(r.core.selected){s=this;this.deselect_all();i.each(r.core.selected,function(w,t){s.select_node(t)});delete r.core.selected;this.set_state(r,v);return false}if(i.isEmptyObject(r.core)){delete r.core;this.set_state(r,v);return false}}if(i.isEmptyObject(r)){r=null;if(v){v.call(this)}this.trigger("set_state");return false}return true}return false},refresh:function(q,p){this._data.core.state=p===true?{}:this.get_state();if(p&&i.isFunction(p)){this._data.core.state=p.call(this,this._data.core.state)}this._cnt=0;this._model.data={"#":{id:"#",parent:null,parents:[],children:[],children_d:[],state:{loaded:false}}};var r=this.get_container_ul()[0].className;if(!q){this.element.html("<ul class='"+r+"'><li class='jstree-initial-node jstree-loading jstree-leaf jstree-last'><i class='jstree-icon jstree-ocl'></i><a class='jstree-anchor' href='#'><i class='jstree-icon jstree-themeicon-hidden'></i>"+this.get_string("Loading ...")+"</a></li></ul>")}this.load_node("#",function(u,t){if(t){this.get_container_ul()[0].className=r;this.set_state(i.extend(true,{},this._data.core.state),function(){this.trigger("refresh")})}this._data.core.state=null})},refresh_node:function(r){r=this.get_node(r);if(!r||r.id==="#"){return false}var t=[],p=[],q=this._data.core.selected.concat([]);p.push(r.id);if(r.state.opened===true){t.push(r.id)}this.get_node(r,true).find(".jstree-open").each(function(){t.push(this.id)});this._load_nodes(p,i.proxy(function(s){this.open_node(t,false,0);this.select_node(this._data.core.selected);this.trigger("refresh_node",{node:r,nodes:s})},this))},set_id:function(s,t){s=this.get_node(s);if(!s||s.id==="#"){return false}var r,q,p=this._model.data;t=t.toString();p[s.parent].children[i.inArray(s.id,p[s.parent].children)]=t;for(r=0,q=s.parents.length;r<q;r++){p[s.parents[r]].children_d[i.inArray(s.id,p[s.parents[r]].children_d)]=t}for(r=0,q=s.children.length;r<q;r++){p[s.children[r]].parent=t}for(r=0,q=s.children_d.length;r<q;r++){p[s.children_d[r]].parents[i.inArray(s.id,p[s.children_d[r]].parents)]=t}r=i.inArray(s.id,this._data.core.selected);if(r!==-1){this._data.core.selected[r]=t}r=this.get_node(s.id,true);if(r){r.attr("id",t)}delete p[s.id];s.id=t;p[t]=s;return true},get_text:function(p){p=this.get_node(p);return(!p||p.id==="#")?false:p.text},set_text:function(r,s){var q,p;if(i.isArray(r)){r=r.slice();for(q=0,p=r.length;q<p;q++){this.set_text(r[q],s)}return true}r=this.get_node(r);if(!r||r.id==="#"){return false}r.text=s;if(this.get_node(r,true).length){this.redraw_node(r.id)}this.trigger("set_text",{obj:r,text:s});return true},get_json:function(t,q,u){t=this.get_node(t||"#");if(!t){return false}if(q&&q.flat&&!u){u=[]}var s={id:t.id,text:t.text,icon:this.get_icon(t),li_attr:t.li_attr,a_attr:t.a_attr,state:{},data:q&&q.no_data?false:t.data},r,p;if(q&&q.flat){s.parent=t.parent}else{s.children=[]}if(!q||!q.no_state){for(r in t.state){if(t.state.hasOwnProperty(r)){s.state[r]=t.state[r]}}}if(q&&q.no_id){delete s.id;if(s.li_attr&&s.li_attr.id){delete s.li_attr.id}}if(q&&q.flat&&t.id!=="#"){u.push(s)}if(!q||!q.no_children){for(r=0,p=t.children.length;r<p;r++){if(q&&q.flat){this.get_json(t.children[r],q,u)}else{s.children.push(this.get_json(t.children[r],q))}}}return q&&q.flat?u:(t.id==="#"?s.children:s)},create_node:function(u,p,w,x,v){if(u===null){u="#"}u=this.get_node(u);if(!u){return false}w=w===e?"last":w;if(!w.toString().match(/^(before|after)$/)&&!v&&!this.is_loaded(u)){return this.load_node(u,function(){this.create_node(u,p,w,x,true)})}if(!p){p={text:this.get_string("New node")}}if(p.text===e){p.text=this.get_string("New node")}var r,t,s,q;if(u.id==="#"){if(w==="before"){w="first"}if(w==="after"){w="last"}}switch(w){case"before":r=this.get_node(u.parent);w=i.inArray(u.id,r.children);u=r;break;case"after":r=this.get_node(u.parent);w=i.inArray(u.id,r.children)+1;u=r;break;case"inside":case"first":w=0;break;case"last":w=u.children.length;break;default:if(!w){w=0}break}if(w>u.children.length){w=u.children.length}if(!p.id){p.id=true}if(!this.check("create_node",p,u,w)){this.settings.core.error.call(this,this._data.core.last_error);return false}if(p.id===true){delete p.id}p=this._parse_model_from_json(p,u.id,u.parents.concat());if(!p){return false}r=this.get_node(p);t=[];t.push(p);t=t.concat(r.children_d);this.trigger("model",{nodes:t,parent:u.id});u.children_d=u.children_d.concat(t);for(s=0,q=u.parents.length;s<q;s++){this._model.data[u.parents[s]].children_d=this._model.data[u.parents[s]].children_d.concat(t)}p=r;r=[];for(s=0,q=u.children.length;s<q;s++){r[s>=w?s+1:s]=u.children[s]}r[w]=p.id;u.children=r;this.redraw_node(u,true);if(x){x.call(this,this.get_node(p))}this.trigger("create_node",{node:this.get_node(p),parent:u.id,position:w});return p.id},rename_node:function(s,t){var r,q,p;if(i.isArray(s)){s=s.slice();for(r=0,q=s.length;r<q;r++){this.rename_node(s[r],t)}return true}s=this.get_node(s);if(!s||s.id==="#"){return false}p=s.text;if(!this.check("rename_node",s,this.get_parent(s),t)){this.settings.core.error.call(this,this._data.core.last_error);return false}this.set_text(s,t);this.trigger("rename_node",{node:s,text:t,old:p});return true},delete_node:function(s){var w,v,x,z,t,u,r,q,p,y;if(i.isArray(s)){s=s.slice();for(w=0,v=s.length;w<v;w++){this.delete_node(s[w])}return true}s=this.get_node(s);if(!s||s.id==="#"){return false}x=this.get_node(s.parent);z=i.inArray(s.id,x.children);y=false;if(!this.check("delete_node",s,x,z)){this.settings.core.error.call(this,this._data.core.last_error);return false}if(z!==-1){x.children=i.vakata.array_remove(x.children,z)}t=s.children_d.concat([]);t.push(s.id);for(q=0,p=t.length;q<p;q++){for(u=0,r=s.parents.length;u<r;u++){z=i.inArray(t[q],this._model.data[s.parents[u]].children_d);if(z!==-1){this._model.data[s.parents[u]].children_d=i.vakata.array_remove(this._model.data[s.parents[u]].children_d,z)}}if(this._model.data[t[q]].state.selected){y=true;z=i.inArray(t[q],this._data.core.selected);if(z!==-1){this._data.core.selected=i.vakata.array_remove(this._data.core.selected,z)}}}this.trigger("delete_node",{node:s,parent:x.id});if(y){this.trigger("changed",{action:"delete_node",node:s,selected:this._data.core.selected,parent:x.id})}for(q=0,p=t.length;q<p;q++){delete this._model.data[t[q]]}this.redraw_node(x,true);return true},check:function(p,t,s,v,r){t=t&&t.id?t:this.get_node(t);s=s&&s.id?s:this.get_node(s);var q=p.match(/^move_node|copy_node|create_node$/i)?s:t,u=this.settings.core.check_callback;if(p==="move_node"||p==="copy_node"){if((!r||!r.is_multi)&&(t.id===s.id||i.inArray(t.id,s.children)===v||i.inArray(s.id,t.children_d)!==-1)){this._data.core.last_error={error:"check",plugin:"core",id:"core_01",reason:"Moving parent inside child",data:JSON.stringify({chk:p,pos:v,obj:t&&t.id?t.id:false,par:s&&s.id?s.id:false})};return false}}if(q&&q.data){q=q.data}if(q&&q.functions&&(q.functions[p]===false||q.functions[p]===true)){if(q.functions[p]===false){this._data.core.last_error={error:"check",plugin:"core",id:"core_02",reason:"Node data prevents function: "+p,data:JSON.stringify({chk:p,pos:v,obj:t&&t.id?t.id:false,par:s&&s.id?s.id:false})}}return q.functions[p]}if(u===false||(i.isFunction(u)&&u.call(this,p,t,s,v,r)===false)||(u&&u[p]===false)){this._data.core.last_error={error:"check",plugin:"core",id:"core_03",reason:"User config for core.check_callback prevents function: "+p,data:JSON.stringify({chk:p,pos:v,obj:t&&t.id?t.id:false,par:s&&s.id?s.id:false})};return false}return true},last_error:function(){return this._data.core.last_error},move_node:function(y,A,t,r,z){var w,v,x,q,H,I,s,u,G,F,E,D,C,B;A=this.get_node(A);t=t===e?0:t;if(!A){return false}if(!t.toString().match(/^(before|after)$/)&&!z&&!this.is_loaded(A)){return this.load_node(A,function(){this.move_node(y,A,t,r,true)})}if(i.isArray(y)){y=y.reverse().slice();for(w=0,v=y.length;w<v;w++){this.move_node(y[w],A,t,r,z)}return true}y=y&&y.id?y:this.get_node(y);if(!y||y.id==="#"){return false}x=(y.parent||"#").toString();H=(!t.toString().match(/^(before|after)$/)||A.id==="#")?A:this.get_node(A.parent);I=y.instance?y.instance:(this._model.data[y.id]?this:i.jstree.reference(y.id));s=!I||!I._id||(this._id!==I._id);q=I&&I._id&&x&&I._model.data[x]&&I._model.data[x].children?i.inArray(y.id,I._model.data[x].children):-1;if(s){if(this.copy_node(y,A,t,r,z)){if(I){I.delete_node(y)}return true}return false}if(H.id==="#"){if(t==="before"){t="first"}if(t==="after"){t="last"}}switch(t){case"before":t=i.inArray(A.id,H.children);break;case"after":t=i.inArray(A.id,H.children)+1;break;case"inside":case"first":t=0;break;case"last":t=H.children.length;break;default:if(!t){t=0}break}if(t>H.children.length){t=H.children.length}if(!this.check("move_node",y,H,t,{core:true,is_multi:(I&&I._id&&I._id!==this._id),is_foreign:(!I||!I._id)})){this.settings.core.error.call(this,this._data.core.last_error);return false}if(y.parent===H.id){u=H.children.concat();G=i.inArray(y.id,u);if(G!==-1){u=i.vakata.array_remove(u,G);if(t>G){t--}}G=[];for(F=0,E=u.length;F<E;F++){G[F>=t?F+1:F]=u[F]}G[t]=y.id;H.children=G;this._node_changed(H.id);this.redraw(H.id==="#")}else{G=y.children_d.concat();G.push(y.id);for(F=0,E=y.parents.length;F<E;F++){u=[];B=I._model.data[y.parents[F]].children_d;for(D=0,C=B.length;D<C;D++){if(i.inArray(B[D],G)===-1){u.push(B[D])}}I._model.data[y.parents[F]].children_d=u}I._model.data[x].children=i.vakata.array_remove_item(I._model.data[x].children,y.id);for(F=0,E=H.parents.length;F<E;F++){this._model.data[H.parents[F]].children_d=this._model.data[H.parents[F]].children_d.concat(G)}u=[];for(F=0,E=H.children.length;F<E;F++){u[F>=t?F+1:F]=H.children[F]}u[t]=y.id;H.children=u;H.children_d.push(y.id);H.children_d=H.children_d.concat(y.children_d);y.parent=H.id;G=H.parents.concat();G.unshift(H.id);B=y.parents.length;y.parents=G;G=G.concat();for(F=0,E=y.children_d.length;F<E;F++){this._model.data[y.children_d[F]].parents=this._model.data[y.children_d[F]].parents.slice(0,B*-1);Array.prototype.push.apply(this._model.data[y.children_d[F]].parents,G)}this._node_changed(x);this._node_changed(H.id);this.redraw(x==="#"||H.id==="#")}if(r){r.call(this,y,H,t)}this.trigger("move_node",{node:y,parent:H.id,position:t,old_parent:x,old_position:q,is_multi:(I&&I._id&&I._id!==this._id),is_foreign:(!I||!I._id),old_instance:I,new_instance:this});return true},copy_node:function(v,B,D,E,C){var z,y,x,u,t,s,q,A,p,w,r;B=this.get_node(B);D=D===e?0:D;if(!B){return false}if(!D.toString().match(/^(before|after)$/)&&!C&&!this.is_loaded(B)){return this.load_node(B,function(){this.copy_node(v,B,D,E,true)})}if(i.isArray(v)){v=v.reverse().slice();for(z=0,y=v.length;z<y;z++){this.copy_node(v[z],B,D,E,C)}return true}v=v&&v.id?v:this.get_node(v);if(!v||v.id==="#"){return false}A=(v.parent||"#").toString();p=(!D.toString().match(/^(before|after)$/)||B.id==="#")?B:this.get_node(B.parent);w=v.instance?v.instance:(this._model.data[v.id]?this:i.jstree.reference(v.id));r=!w||!w._id||(this._id!==w._id);if(p.id==="#"){if(D==="before"){D="first"}if(D==="after"){D="last"}}switch(D){case"before":D=i.inArray(B.id,p.children);break;case"after":D=i.inArray(B.id,p.children)+1;break;case"inside":case"first":D=0;break;case"last":D=p.children.length;break;default:if(!D){D=0}break}if(D>p.children.length){D=p.children.length}if(!this.check("copy_node",v,p,D,{core:true,is_multi:(w&&w._id&&w._id!==this._id),is_foreign:(!w||!w._id)})){this.settings.core.error.call(this,this._data.core.last_error);return false}q=w?w.get_json(v,{no_id:true,no_data:true,no_state:true}):v;if(!q){return false}if(q.id===true){delete q.id}q=this._parse_model_from_json(q,p.id,p.parents.concat());if(!q){return false}u=this.get_node(q);if(v&&v.state&&v.state.loaded===false){u.state.loaded=false}x=[];x.push(q);x=x.concat(u.children_d);this.trigger("model",{nodes:x,parent:p.id});for(t=0,s=p.parents.length;t<s;t++){this._model.data[p.parents[t]].children_d=this._model.data[p.parents[t]].children_d.concat(x)}x=[];for(t=0,s=p.children.length;t<s;t++){x[t>=D?t+1:t]=p.children[t]}x[D]=u.id;p.children=x;p.children_d.push(u.id);p.children_d=p.children_d.concat(u.children_d);this._node_changed(p.id);this.redraw(p.id==="#");if(E){E.call(this,u,p,D)}this.trigger("copy_node",{node:u,original:v,parent:p.id,position:D,old_parent:A,old_position:w&&w._id&&A&&w._model.data[A]&&w._model.data[A].children?i.inArray(v.id,w._model.data[A].children):-1,is_multi:(w&&w._id&&w._id!==this._id),is_foreign:(!w||!w._id),old_instance:w,new_instance:this});return u.id},cut:function(s){if(!s){s=this._data.core.selected.concat()}if(!i.isArray(s)){s=[s]}if(!s.length){return false}var p=[],t,r,q;for(r=0,q=s.length;r<q;r++){t=this.get_node(s[r]);if(t&&t.id&&t.id!=="#"){p.push(t)}}if(!p.length){return false}d=p;j=this;k="move_node";this.trigger("cut",{node:s})},copy:function(s){if(!s){s=this._data.core.selected.concat()}if(!i.isArray(s)){s=[s]}if(!s.length){return false}var p=[],t,r,q;for(r=0,q=s.length;r<q;r++){t=this.get_node(s[r]);if(t&&t.id&&t.id!=="#"){p.push(t)}}if(!p.length){return false}d=p;j=this;k="copy_node";this.trigger("copy",{node:s})},get_buffer:function(){return{mode:k,node:d,inst:j}},can_paste:function(){return k!==false&&d!==false},paste:function(p,q){p=this.get_node(p);if(!p||!k||!k.match(/^(copy_node|move_node)$/)||!d){return false}if(this[k](d,p,q)){this.trigger("paste",{parent:p.id,node:d,mode:k})}d=false;k=false;j=false},edit:function(p,x){p=this.get_node(p);if(!p){return false}if(this.settings.core.check_callback===false){this._data.core.last_error={error:"check",plugin:"core",id:"core_07",reason:"Could not edit node because of check_callback"};this.settings.core.error.call(this,this._data.core.last_error);return false}x=typeof x==="string"?x:p.text;this.set_text(p,"");p=this._open_to(p);var v=this._data.core.rtl,z=this.element.width(),y=p.children(".jstree-anchor"),B=i("<span>")
+/*
+				oi = obj.children("i:visible"),
+				ai = a.children("i:visible"),
+				w1 = oi.width() * oi.length,
+				w2 = ai.width() * ai.length,
+				*/
+,A=x,r=i("<div />",{css:{position:"absolute",top:"-200px",left:(v?"0px":"-1000px"),visibility:"hidden"}}).appendTo("body"),q=i("<input />",{value:A,"class":"jstree-rename-input",css:{padding:"0",border:"1px solid silver","box-sizing":"border-box",display:"inline-block",height:(this._data.core.li_height)+"px",lineHeight:(this._data.core.li_height)+"px",width:"150px"},blur:i.proxy(function(){var t=B.children(".jstree-rename-input"),s=t.val();if(s===""){s=A}r.remove();B.replaceWith(y);B.remove();this.set_text(p,A);if(this.rename_node(p,i("<div></div>").text(s)[this.settings.core.force_text?"text":"html"]())===false){this.set_text(p,A)}},this),keydown:function(t){var s=t.which;if(s===27){this.value=A}if(s===27||s===13||s===37||s===38||s===39||s===40||s===32){t.stopImmediatePropagation()}if(s===27||s===13){t.preventDefault();this.blur()}},click:function(s){s.stopImmediatePropagation()},mousedown:function(s){s.stopImmediatePropagation()},keyup:function(s){q.width(Math.min(r.text("pW"+this.value).width(),z))},keypress:function(s){if(s.which===13){return false}}}),u={fontFamily:y.css("fontFamily")||"",fontSize:y.css("fontSize")||"",fontWeight:y.css("fontWeight")||"",fontStyle:y.css("fontStyle")||"",fontStretch:y.css("fontStretch")||"",fontVariant:y.css("fontVariant")||"",letterSpacing:y.css("letterSpacing")||"",wordSpacing:y.css("wordSpacing")||""};B.attr("class",y.attr("class")).append(y.contents().clone()).append(q);y.replaceWith(B);r.css(u);q.css(u).width(Math.min(r.text("pW"+q[0].value).width(),z))[0].select()},set_theme:function(r,p){if(!r){return false}if(p===true){var q=this.settings.core.themes.dir;if(!q){q=i.jstree.path+"/themes"}p=q+"/"+r+"/style.css"}if(p&&i.inArray(p,m)===-1){i("head").append('<link rel="stylesheet" href="'+p+'" type="text/css" />');m.push(p)}if(this._data.core.themes.name){this.element.removeClass("jstree-"+this._data.core.themes.name)}this._data.core.themes.name=r;this.element.addClass("jstree-"+r);this.element[this.settings.core.themes.responsive?"addClass":"removeClass"]("jstree-"+r+"-responsive");this.trigger("set_theme",{theme:r})},get_theme:function(){return this._data.core.themes.name},set_theme_variant:function(p){if(this._data.core.themes.variant){this.element.removeClass("jstree-"+this._data.core.themes.name+"-"+this._data.core.themes.variant)}this._data.core.themes.variant=p;if(p){this.element.addClass("jstree-"+this._data.core.themes.name+"-"+this._data.core.themes.variant)}},get_theme_variant:function(){return this._data.core.themes.variant},show_stripes:function(){this._data.core.themes.stripes=true;this.get_container_ul().addClass("jstree-striped")},hide_stripes:function(){this._data.core.themes.stripes=false;this.get_container_ul().removeClass("jstree-striped")},toggle_stripes:function(){if(this._data.core.themes.stripes){this.hide_stripes()}else{this.show_stripes()}},show_dots:function(){this._data.core.themes.dots=true;this.get_container_ul().removeClass("jstree-no-dots")},hide_dots:function(){this._data.core.themes.dots=false;this.get_container_ul().addClass("jstree-no-dots")},toggle_dots:function(){if(this._data.core.themes.dots){this.hide_dots()}else{this.show_dots()}},show_icons:function(){this._data.core.themes.icons=true;this.get_container_ul().removeClass("jstree-no-icons")},hide_icons:function(){this._data.core.themes.icons=false;this.get_container_ul().addClass("jstree-no-icons")},toggle_icons:function(){if(this._data.core.themes.icons){this.hide_icons()}else{this.show_icons()}},set_icon:function(t,r){var s,q,u,p;if(i.isArray(t)){t=t.slice();for(s=0,q=t.length;s<q;s++){this.set_icon(t[s],r)}return true}t=this.get_node(t);if(!t||t.id==="#"){return false}p=t.icon;t.icon=r;u=this.get_node(t,true).children(".jstree-anchor").children(".jstree-themeicon");if(r===false){this.hide_icon(t)}else{if(r===true){u.removeClass("jstree-themeicon-custom "+p).css("background","").removeAttr("rel")}else{if(r.indexOf("/")===-1&&r.indexOf(".")===-1){u.removeClass(p).css("background","");u.addClass(r+" jstree-themeicon-custom").attr("rel",r)}else{u.removeClass(p).css("background","");u.addClass("jstree-themeicon-custom").css("background","url('"+r+"') center center no-repeat").attr("rel",r)}}}return true},get_icon:function(p){p=this.get_node(p);return(!p||p.id==="#")?false:p.icon},hide_icon:function(r){var q,p;if(i.isArray(r)){r=r.slice();for(q=0,p=r.length;q<p;q++){this.hide_icon(r[q])}return true}r=this.get_node(r);if(!r||r==="#"){return false}r.icon=false;this.get_node(r,true).children(".jstree-anchor").children(".jstree-themeicon").addClass("jstree-themeicon-hidden");return true},show_icon:function(r){var q,p,s;if(i.isArray(r)){r=r.slice();for(q=0,p=r.length;q<p;q++){this.show_icon(r[q])}return true}r=this.get_node(r);if(!r||r==="#"){return false}s=this.get_node(r,true);r.icon=s.length?s.children(".jstree-anchor").children(".jstree-themeicon").attr("rel"):true;if(!r.icon){r.icon=true}s.children(".jstree-anchor").children(".jstree-themeicon").removeClass("jstree-themeicon-hidden");return true}};i.vakata={};i.vakata.attributes=function(q,r){q=i(q)[0];var p=r?{}:[];if(q&&q.attributes){i.each(q.attributes,function(t,s){if(i.inArray(s.nodeName.toLowerCase(),["style","contenteditable","hasfocus","tabindex"])!==-1){return}if(s.nodeValue!==null&&i.trim(s.nodeValue)!==""){if(r){p[s.nodeName]=s.nodeValue}else{p.push(s.nodeName)}}})}return p};i.vakata.array_unique=function(t){var q=[],s,r,p;for(s=0,p=t.length;s<p;s++){for(r=0;r<=s;r++){if(t[s]===t[r]){break}}if(r===s){q.push(t[s])}}return q};i.vakata.array_remove=function(s,r,q){var p=s.slice((q||r)+1||s.length);s.length=r<0?s.length+r:r;s.push.apply(s,p);return s};i.vakata.array_remove_item=function(r,q){var p=i.inArray(q,r);return p!==-1?i.vakata.array_remove(r,p):r};var h=document.createElement("I");h.className="jstree-icon jstree-checkbox";i.jstree.defaults.checkbox={visible:true,three_state:true,whole_node:true,keep_selected_style:true,cascade:"",tie_selection:true};i.jstree.plugins.checkbox=function(p,q){this.bind=function(){q.bind.call(this);this._data.checkbox.uto=false;this._data.checkbox.selected=[];if(this.settings.checkbox.three_state){this.settings.checkbox.cascade="up+down+undetermined"}this.element.on("init.jstree",i.proxy(function(){this._data.checkbox.visible=this.settings.checkbox.visible;if(!this.settings.checkbox.keep_selected_style){this.element.addClass("jstree-checkbox-no-clicked")}if(this.settings.checkbox.tie_selection){this.element.addClass("jstree-checkbox-selection")}},this)).on("loading.jstree",i.proxy(function(){this[this._data.checkbox.visible?"show_checkboxes":"hide_checkboxes"]()},this));if(this.settings.checkbox.cascade.indexOf("undetermined")!==-1){this.element.on("changed.jstree uncheck_node.jstree check_node.jstree uncheck_all.jstree check_all.jstree move_node.jstree copy_node.jstree redraw.jstree open_node.jstree",i.proxy(function(){if(this._data.checkbox.uto){clearTimeout(this._data.checkbox.uto)}this._data.checkbox.uto=setTimeout(i.proxy(this._undetermined,this),50)},this))}if(!this.settings.checkbox.tie_selection){this.element.on("model.jstree",i.proxy(function(w,u){var r=this._model.data,v=r[u.parent],x=u.nodes,t,s;for(t=0,s=x.length;t<s;t++){r[x[t]].state.checked=(r[x[t]].original&&r[x[t]].original.state&&r[x[t]].original.state.checked);if(r[x[t]].state.checked){this._data.checkbox.selected.push(x[t])}}},this))}if(this.settings.checkbox.cascade.indexOf("up")!==-1||this.settings.checkbox.cascade.indexOf("down")!==-1){this.element.on("model.jstree",i.proxy(function(C,z){var u=this._model.data,r=u[z.parent],B=z.nodes,G=[],D,A,x,w,v,y,F=this.settings.checkbox.cascade,E=this.settings.checkbox.tie_selection;if(F.indexOf("down")!==-1){if(r.state[E?"selected":"checked"]){for(A=0,x=B.length;A<x;A++){u[B[A]].state[E?"selected":"checked"]=true}this._data[E?"core":"checkbox"].selected=this._data[E?"core":"checkbox"].selected.concat(B)}else{for(A=0,x=B.length;A<x;A++){if(u[B[A]].state[E?"selected":"checked"]){for(w=0,v=u[B[A]].children_d.length;w<v;w++){u[u[B[A]].children_d[w]].state[E?"selected":"checked"]=true}this._data[E?"core":"checkbox"].selected=this._data[E?"core":"checkbox"].selected.concat(u[B[A]].children_d)}}}}if(F.indexOf("up")!==-1){for(A=0,x=r.children_d.length;A<x;A++){if(!u[r.children_d[A]].children.length){G.push(u[r.children_d[A]].parent)}}G=i.vakata.array_unique(G);for(w=0,v=G.length;w<v;w++){r=u[G[w]];while(r&&r.id!=="#"){D=0;for(A=0,x=r.children.length;A<x;A++){D+=u[r.children[A]].state[E?"selected":"checked"]}if(D===x){r.state[E?"selected":"checked"]=true;this._data[E?"core":"checkbox"].selected.push(r.id);y=this.get_node(r,true);if(y&&y.length){y.children(".jstree-anchor").addClass(E?"jstree-clicked":"jstree-checked")}}else{break}r=this.get_node(r.parent)}}}this._data[E?"core":"checkbox"].selected=i.vakata.array_unique(this._data[E?"core":"checkbox"].selected)},this)).on(this.settings.checkbox.tie_selection?"select_node.jstree":"check_node.jstree",i.proxy(function(A,y){var x=y.node,r=this._model.data,B=this.get_node(x.parent),u=this.get_node(x,true),z,v,C,w,E=this.settings.checkbox.cascade,D=this.settings.checkbox.tie_selection;if(E.indexOf("down")!==-1){this._data[D?"core":"checkbox"].selected=i.vakata.array_unique(this._data[D?"core":"checkbox"].selected.concat(x.children_d));for(z=0,v=x.children_d.length;z<v;z++){w=r[x.children_d[z]];w.state[D?"selected":"checked"]=true;if(w&&w.original&&w.original.state&&w.original.state.undetermined){w.original.state.undetermined=false}}}if(E.indexOf("up")!==-1){while(B&&B.id!=="#"){C=0;for(z=0,v=B.children.length;z<v;z++){C+=r[B.children[z]].state[D?"selected":"checked"]}if(C===v){B.state[D?"selected":"checked"]=true;this._data[D?"core":"checkbox"].selected.push(B.id);w=this.get_node(B,true);if(w&&w.length){w.children(".jstree-anchor").addClass(D?"jstree-clicked":"jstree-checked")}}else{break}B=this.get_node(B.parent)}}if(E.indexOf("down")!==-1&&u.length){u.find(".jstree-anchor").addClass(D?"jstree-clicked":"jstree-checked")}},this)).on(this.settings.checkbox.tie_selection?"deselect_all.jstree":"uncheck_all.jstree",i.proxy(function(x,v){var w=this.get_node("#"),r=this._model.data,u,s,t;for(u=0,s=w.children_d.length;u<s;u++){t=r[w.children_d[u]];if(t&&t.original&&t.original.state&&t.original.state.undetermined){t.original.state.undetermined=false}}},this)).on(this.settings.checkbox.tie_selection?"deselect_node.jstree":"uncheck_node.jstree",i.proxy(function(z,w){var v=w.node,r=this.get_node(v,true),x,u,y,B=this.settings.checkbox.cascade,A=this.settings.checkbox.tie_selection;if(v&&v.original&&v.original.state&&v.original.state.undetermined){v.original.state.undetermined=false}if(B.indexOf("down")!==-1){for(x=0,u=v.children_d.length;x<u;x++){y=this._model.data[v.children_d[x]];y.state[A?"selected":"checked"]=false;if(y&&y.original&&y.original.state&&y.original.state.undetermined){y.original.state.undetermined=false}}}if(B.indexOf("up")!==-1){for(x=0,u=v.parents.length;x<u;x++){y=this._model.data[v.parents[x]];y.state[A?"selected":"checked"]=false;if(y&&y.original&&y.original.state&&y.original.state.undetermined){y.original.state.undetermined=false}y=this.get_node(v.parents[x],true);if(y&&y.length){y.children(".jstree-anchor").removeClass(A?"jstree-clicked":"jstree-checked")}}}y=[];for(x=0,u=this._data[A?"core":"checkbox"].selected.length;x<u;x++){if((B.indexOf("down")===-1||i.inArray(this._data[A?"core":"checkbox"].selected[x],v.children_d)===-1)&&(B.indexOf("up")===-1||i.inArray(this._data[A?"core":"checkbox"].selected[x],v.parents)===-1)){y.push(this._data[A?"core":"checkbox"].selected[x])}}this._data[A?"core":"checkbox"].selected=i.vakata.array_unique(y);if(B.indexOf("down")!==-1&&r.length){r.find(".jstree-anchor").removeClass(A?"jstree-clicked":"jstree-checked")}},this))}if(this.settings.checkbox.cascade.indexOf("up")!==-1){this.element.on("delete_node.jstree",i.proxy(function(y,v){var r=this.get_node(v.parent),s=this._model.data,w,u,z,x,A=this.settings.checkbox.tie_selection;while(r&&r.id!=="#"){z=0;for(w=0,u=r.children.length;w<u;w++){z+=s[r.children[w]].state[A?"selected":"checked"]}if(z===u){r.state[A?"selected":"checked"]=true;this._data[A?"core":"checkbox"].selected.push(r.id);x=this.get_node(r,true);if(x&&x.length){x.children(".jstree-anchor").addClass(A?"jstree-clicked":"jstree-checked")}}else{break}r=this.get_node(r.parent)}},this)).on("move_node.jstree",i.proxy(function(B,z){var v=z.is_multi,A=z.old_parent,r=this.get_node(z.parent),u=this._model.data,s,C,y,w,x,D=this.settings.checkbox.tie_selection;if(!v){s=this.get_node(A);while(s&&s.id!=="#"){C=0;for(y=0,w=s.children.length;y<w;y++){C+=u[s.children[y]].state[D?"selected":"checked"]}if(C===w){s.state[D?"selected":"checked"]=true;this._data[D?"core":"checkbox"].selected.push(s.id);x=this.get_node(s,true);if(x&&x.length){x.children(".jstree-anchor").addClass(D?"jstree-clicked":"jstree-checked")}}else{break}s=this.get_node(s.parent)}}s=r;while(s&&s.id!=="#"){C=0;for(y=0,w=s.children.length;y<w;y++){C+=u[s.children[y]].state[D?"selected":"checked"]}if(C===w){if(!s.state[D?"selected":"checked"]){s.state[D?"selected":"checked"]=true;this._data[D?"core":"checkbox"].selected.push(s.id);x=this.get_node(s,true);if(x&&x.length){x.children(".jstree-anchor").addClass(D?"jstree-clicked":"jstree-checked")}}}else{if(s.state[D?"selected":"checked"]){s.state[D?"selected":"checked"]=false;this._data[D?"core":"checkbox"].selected=i.vakata.array_remove_item(this._data[D?"core":"checkbox"].selected,s.id);x=this.get_node(s,true);if(x&&x.length){x.children(".jstree-anchor").removeClass(D?"jstree-clicked":"jstree-checked")}}else{break}}s=this.get_node(s.parent)}},this))}};this._undetermined=function(){var w,u,r=this._model.data,v=this.settings.checkbox.tie_selection,y=this._data[v?"core":"checkbox"].selected,z=[],x=this;for(w=0,u=y.length;w<u;w++){if(r[y[w]]&&r[y[w]].parents){z=z.concat(r[y[w]].parents)}}this.element.find(".jstree-closed").not(":has(.jstree-children)").each(function(){var s=x.get_node(this),t;if(!s.state.loaded){if(s.original&&s.original.state&&s.original.state.undetermined&&s.original.state.undetermined===true){z.push(s.id);z=z.concat(s.parents)}}else{for(w=0,u=s.children_d.length;w<u;w++){t=r[s.children_d[w]];if(!t.state.loaded&&t.original&&t.original.state&&t.original.state.undetermined&&t.original.state.undetermined===true){z.push(t.id);z=z.concat(t.parents)}}}});z=i.vakata.array_unique(z);z=i.vakata.array_remove_item(z,"#");this.element.find(".jstree-undetermined").removeClass("jstree-undetermined");for(w=0,u=z.length;w<u;w++){if(!r[z[w]].state[v?"selected":"checked"]){y=this.get_node(z[w],true);if(y&&y.length){y.children(".jstree-anchor").children(".jstree-checkbox").addClass("jstree-undetermined")}}}};this.redraw_node=function(w,r,v){w=q.redraw_node.call(this,w,r,v);if(w){var u,s,t=null;for(u=0,s=w.childNodes.length;u<s;u++){if(w.childNodes[u]&&w.childNodes[u].className&&w.childNodes[u].className.indexOf("jstree-anchor")!==-1){t=w.childNodes[u];break}}if(t){if(!this.settings.checkbox.tie_selection&&this._model.data[w.id].state.checked){t.className+=" jstree-checked"}t.insertBefore(h.cloneNode(false),t.childNodes[0])}}if(!v&&this.settings.checkbox.cascade.indexOf("undetermined")!==-1){if(this._data.checkbox.uto){clearTimeout(this._data.checkbox.uto)}this._data.checkbox.uto=setTimeout(i.proxy(this._undetermined,this),50)}return w};this.show_checkboxes=function(){this._data.core.themes.checkboxes=true;this.get_container_ul().removeClass("jstree-no-checkboxes")};this.hide_checkboxes=function(){this._data.core.themes.checkboxes=false;this.get_container_ul().addClass("jstree-no-checkboxes")};this.toggle_checkboxes=function(){if(this._data.core.themes.checkboxes){this.hide_checkboxes()}else{this.show_checkboxes()}};this.is_undetermined=function(y){y=this.get_node(y);var x=this.settings.checkbox.cascade,w,u,v=this.settings.checkbox.tie_selection,z=this._data[v?"core":"checkbox"].selected,r=this._model.data;if(!y||y.state[v?"selected":"checked"]===true||x.indexOf("undetermined")===-1||(x.indexOf("down")===-1&&x.indexOf("up")===-1)){return false}if(!y.state.loaded&&y.original.state.undetermined===true){return true}for(w=0,u=y.children_d.length;w<u;w++){if(i.inArray(y.children_d[w],z)!==-1||(!r[y.children_d[w]].state.loaded&&r[y.children_d[w]].original.state.undetermined)){return true}}return false};this.activate_node=function(s,r){if(this.settings.checkbox.tie_selection&&(this.settings.checkbox.whole_node||i(r.target).hasClass("jstree-checkbox"))){r.ctrlKey=true}if(this.settings.checkbox.tie_selection||(!this.settings.checkbox.whole_node&&!i(r.target).hasClass("jstree-checkbox"))){return q.activate_node.call(this,s,r)}if(this.is_checked(s)){this.uncheck_node(s,r)}else{this.check_node(s,r)}this.trigger("activate_node",{node:this.get_node(s)})};this.check_node=function(v,u){if(this.settings.checkbox.tie_selection){return this.select_node(v,false,true,u)}var w,t,r,s;if(i.isArray(v)){v=v.slice();for(t=0,r=v.length;t<r;t++){this.check_node(v[t],u)}return true}v=this.get_node(v);if(!v||v.id==="#"){return false}w=this.get_node(v,true);if(!v.state.checked){v.state.checked=true;this._data.checkbox.selected.push(v.id);if(w&&w.length){w.children(".jstree-anchor").addClass("jstree-checked")}this.trigger("check_node",{node:v,selected:this._data.checkbox.selected,event:u})}};this.uncheck_node=function(u,t){if(this.settings.checkbox.tie_selection){return this.deselect_node(u,false,t)}var s,r,v;if(i.isArray(u)){u=u.slice();for(s=0,r=u.length;s<r;s++){this.uncheck_node(u[s],t)}return true}u=this.get_node(u);if(!u||u.id==="#"){return false}v=this.get_node(u,true);if(u.state.checked){u.state.checked=false;this._data.checkbox.selected=i.vakata.array_remove_item(this._data.checkbox.selected,u.id);if(v.length){v.children(".jstree-anchor").removeClass("jstree-checked")}this.trigger("uncheck_node",{node:u,selected:this._data.checkbox.selected,event:t})}};this.check_all=function(){if(this.settings.checkbox.tie_selection){return this.select_all()}var t=this._data.checkbox.selected.concat([]),s,r;this._data.checkbox.selected=this._model.data["#"].children_d.concat();for(s=0,r=this._data.checkbox.selected.length;s<r;s++){if(this._model.data[this._data.checkbox.selected[s]]){this._model.data[this._data.checkbox.selected[s]].state.checked=true}}this.redraw(true);this.trigger("check_all",{selected:this._data.checkbox.selected})};this.uncheck_all=function(){if(this.settings.checkbox.tie_selection){return this.deselect_all()}var t=this._data.checkbox.selected.concat([]),s,r;for(s=0,r=this._data.checkbox.selected.length;s<r;s++){if(this._model.data[this._data.checkbox.selected[s]]){this._model.data[this._data.checkbox.selected[s]].state.checked=false}}this._data.checkbox.selected=[];this.element.find(".jstree-checked").removeClass("jstree-checked");this.trigger("uncheck_all",{selected:this._data.checkbox.selected,node:t})};this.is_checked=function(r){if(this.settings.checkbox.tie_selection){return this.is_selected(r)}r=this.get_node(r);if(!r||r.id==="#"){return false}return r.state.checked};this.get_checked=function(r){if(this.settings.checkbox.tie_selection){return this.get_selected(r)}return r?i.map(this._data.checkbox.selected,i.proxy(function(s){return this.get_node(s)},this)):this._data.checkbox.selected};this.get_top_checked=function(w){if(this.settings.checkbox.tie_selection){return this.get_top_selected(w)}var v=this.get_checked(true),x={},u,t,s,r;for(u=0,t=v.length;u<t;u++){x[v[u].id]=v[u]}for(u=0,t=v.length;u<t;u++){for(s=0,r=v[u].children_d.length;s<r;s++){if(x[v[u].children_d[s]]){delete x[v[u].children_d[s]]}}}v=[];for(u in x){if(x.hasOwnProperty(u)){v.push(u)}}return w?i.map(v,i.proxy(function(y){return this.get_node(y)},this)):v};this.get_bottom_checked=function(u){if(this.settings.checkbox.tie_selection){return this.get_bottom_selected(u)}var t=this.get_checked(true),v=[],s,r;for(s=0,r=t.length;s<r;s++){if(!t[s].children.length){v.push(t[s].id)}}return u?i.map(v,i.proxy(function(w){return this.get_node(w)},this)):v}};i.jstree.defaults.contextmenu={select_node:true,show_at_node:true,items:function(q,p){return{create:{separator_before:false,separator_after:true,_disabled:false,label:"Create",action:function(s){var r=i.jstree.reference(s.reference),t=r.get_node(s.reference);r.create_node(t,{},"last",function(u){setTimeout(function(){r.edit(u)},0)})}},rename:{separator_before:false,separator_after:false,_disabled:false,label:"Rename",action:function(s){var r=i.jstree.reference(s.reference),t=r.get_node(s.reference);r.edit(t)}},remove:{separator_before:false,icon:false,separator_after:false,_disabled:false,label:"Delete",action:function(s){var r=i.jstree.reference(s.reference),t=r.get_node(s.reference);if(r.is_selected(t)){r.delete_node(r.get_selected())}else{r.delete_node(t)}}},ccp:{separator_before:true,icon:false,separator_after:false,label:"Edit",action:false,submenu:{cut:{separator_before:false,separator_after:false,label:"Cut",action:function(s){var r=i.jstree.reference(s.reference),t=r.get_node(s.reference);if(r.is_selected(t)){r.cut(r.get_selected())}else{r.cut(t)}}},copy:{separator_before:false,icon:false,separator_after:false,label:"Copy",action:function(s){var r=i.jstree.reference(s.reference),t=r.get_node(s.reference);if(r.is_selected(t)){r.copy(r.get_selected())}else{r.copy(t)}}},paste:{separator_before:false,icon:false,_disabled:function(r){return !i.jstree.reference(r.reference).can_paste()},separator_after:false,label:"Paste",action:function(s){var r=i.jstree.reference(s.reference),t=r.get_node(s.reference);r.paste(t)}}}}}}};i.jstree.plugins.contextmenu=function(p,q){this.bind=function(){q.bind.call(this);var r=0;this.element.on("contextmenu.jstree",".jstree-anchor",i.proxy(function(s){s.preventDefault();r=s.ctrlKey?s.timeStamp:0;if(!this.is_loading(s.currentTarget)){this.show_contextmenu(s.currentTarget,s.pageX,s.pageY,s)}},this)).on("click.jstree",".jstree-anchor",i.proxy(function(s){if(this._data.contextmenu.visible&&(!r||s.timeStamp-r>250)){i.vakata.context.hide()}},this));i(document).on("context_hide.vakata",i.proxy(function(){this._data.contextmenu.visible=false},this))};this.teardown=function(){if(this._data.contextmenu.visible){i.vakata.context.hide()}q.teardown.call(this)};this.show_contextmenu=function(u,B,z,v){u=this.get_node(u);if(!u||u.id==="#"){return false}var C=this.settings.contextmenu,w=this.get_node(u,true),A=w.children(".jstree-anchor"),r=false,t=false;if(C.show_at_node||B===e||z===e){r=A.offset();B=r.left;z=r.top+this._data.core.li_height}if(this.settings.contextmenu.select_node&&!this.is_selected(u)){this.activate_node(u,v)}t=C.items;if(i.isFunction(t)){t=t.call(this,u,i.proxy(function(s){this._show_contextmenu(u,B,z,s)},this))}if(i.isPlainObject(t)){this._show_contextmenu(u,B,z,t)}};this._show_contextmenu=function(u,r,w,t){var v=this.get_node(u,true),s=v.children(".jstree-anchor");i(document).one("context_show.vakata",i.proxy(function(z,y){var x="jstree-contextmenu jstree-"+this.get_theme()+"-contextmenu";i(y.element).addClass(x)},this));this._data.contextmenu.visible=true;i.vakata.context.show(s,{x:r,y:w},t);this.trigger("show_contextmenu",{node:u,x:r,y:w})}};(function(q){var r=false,p={element:false,reference:false,position_x:0,position_y:0,items:[],html:"",is_visible:false};q.vakata.context={settings:{hide_onmouseleave:0,icons:true},_trigger:function(s){q(document).triggerHandler("context_"+s+".vakata",{reference:p.reference,element:p.element,position:{x:p.position_x,y:p.position_y}})},_execute:function(s){s=p.items[s];return s&&(!s._disabled||(q.isFunction(s._disabled)&&!s._disabled({item:s,reference:p.reference,element:p.element})))&&s.action?s.action.call(null,{item:s,reference:p.reference,element:p.element,position:{x:p.position_x,y:p.position_y}}):false},_parse:function(w,u){if(!w){return false}if(!u){p.html="";p.items=[]}var v="",s=false,t;if(u){v+="<ul>"}q.each(w,function(x,y){if(!y){return true}p.items.push(y);if(!s&&y.separator_before){v+="<li class='vakata-context-separator'><a href='#' "+(q.vakata.context.settings.icons?"":'style="margin-left:0px;"')+"> </a></li>"}s=false;v+="<li class='"+(y._class||"")+(y._disabled===true||(q.isFunction(y._disabled)&&y._disabled({item:y,reference:p.reference,element:p.element}))?" vakata-contextmenu-disabled ":"")+"' "+(y.shortcut?" data-shortcut='"+y.shortcut+"' ":"")+">";v+="<a href='#' rel='"+(p.items.length-1)+"'>";if(q.vakata.context.settings.icons){v+="<i ";if(y.icon){if(y.icon.indexOf("/")!==-1||y.icon.indexOf(".")!==-1){v+=" style='background:url(\""+y.icon+"\") center center no-repeat' "}else{v+=" class='"+y.icon+"' "}}v+="></i><span class='vakata-contextmenu-sep'> </span>"}v+=(q.isFunction(y.label)?y.label({item:x,reference:p.reference,element:p.element}):y.label)+(y.shortcut?' <span class="vakata-contextmenu-shortcut vakata-contextmenu-shortcut-'+y.shortcut+'">'+(y.shortcut_label||"")+"</span>":"")+"</a>";if(y.submenu){t=q.vakata.context._parse(y.submenu,true);if(t){v+=t}}v+="</li>";if(y.separator_after){v+="<li class='vakata-context-separator'><a href='#' 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38:if(p.is_visible){u=p.element.find("ul:visible").addBack().last().children(".vakata-context-hover").removeClass("vakata-context-hover").prevAll("li:not(.vakata-context-separator)").first();if(!u.length){u=p.element.find("ul:visible").addBack().last().children("li:not(.vakata-context-separator)").last()}u.addClass("vakata-context-hover").children("a").focus();t.stopImmediatePropagation();t.preventDefault()}break;case 39:if(p.is_visible){p.element.find(".vakata-context-hover").last().children("ul").show().children("li:not(.vakata-context-separator)").removeClass("vakata-context-hover").first().addClass("vakata-context-hover").children("a").focus();t.stopImmediatePropagation();t.preventDefault()}break;case 40:if(p.is_visible){u=p.element.find("ul:visible").addBack().last().children(".vakata-context-hover").removeClass("vakata-context-hover").nextAll("li:not(.vakata-context-separator)").first();if(!u.length){u=p.element.find("ul:visible").addBack().last().children("li:not(.vakata-context-separator)").first()}u.addClass("vakata-context-hover").children("a").focus();t.stopImmediatePropagation();t.preventDefault()}break;case 27:q.vakata.context.hide();t.preventDefault();break;default:break}}).on("keydown",function(u){u.preventDefault();var t=p.element.find(".vakata-contextmenu-shortcut-"+u.which).parent();if(t.parent().not(".vakata-context-disabled")){t.mouseup()}}).appendTo("body");q(document).on("mousedown",function(t){if(p.is_visible&&!q.contains(p.element[0],t.target)){q.vakata.context.hide()}}).on("context_show.vakata",function(u,t){p.element.find("li:has(ul)").children("a").addClass("vakata-context-parent");if(r){p.element.addClass("vakata-context-rtl").css("direction","rtl")}p.element.find("ul").hide().end()})})}(i));i.jstree.defaults.dnd={copy:true,open_timeout:500,is_draggable:true,check_while_dragging:true,always_copy:false,inside_pos:0};i.jstree.plugins.dnd=function(p,q){this.bind=function(){q.bind.call(this);this.element.on("mousedown.jstree touchstart.jstree",".jstree-anchor",i.proxy(function(t){var s=this.get_node(t.target),r=this.is_selected(s)?this.get_selected().length:1;if(s&&s.id&&s.id!=="#"&&(t.which===1||t.type==="touchstart")&&(this.settings.dnd.is_draggable===true||(i.isFunction(this.settings.dnd.is_draggable)&&this.settings.dnd.is_draggable.call(this,(r>1?this.get_selected(true):[s]))))){this.element.trigger("mousedown.jstree");return i.vakata.dnd.start(t,{jstree:true,origin:this,obj:this.get_node(s,true),nodes:r>1?this.get_selected():[s.id]},'<div id="jstree-dnd" class="jstree-'+this.get_theme()+(this.settings.core.themes.responsive?" jstree-dnd-responsive":"")+'"><i class="jstree-icon jstree-er"></i>'+(r>1?r+" "+this.get_string("nodes"):this.get_text(t.currentTarget,true))+'<ins class="jstree-copy" style="display:none;">+</ins></div>')}},this))}};i(function(){var s=false,r=false,q=false,p=i('<div id="jstree-marker"> </div>').hide().appendTo("body");i(document).bind("dnd_start.vakata",function(u,t){s=false}).bind("dnd_move.vakata",function(L,N){if(q){clearTimeout(q)}if(!N||!N.data||!N.data.jstree){return}if(N.event.target.id&&N.event.target.id==="jstree-marker"){return}var u=i.jstree.reference(N.event.target),x=false,M=false,v=false,I,D,K,E,J,F,C,B,A,z,G,H,y,w;if(u&&u._data&&u._data.dnd){p.attr("class","jstree-"+u.get_theme()+(u.settings.core.themes.responsive?" jstree-dnd-responsive":""));N.helper.children().attr("class","jstree-"+u.get_theme()+(u.settings.core.themes.responsive?" jstree-dnd-responsive":"")).find(".jstree-copy:eq(0)")[N.data.origin&&(N.data.origin.settings.dnd.always_copy||(N.data.origin.settings.dnd.copy&&(N.event.metaKey||N.event.ctrlKey)))?"show":"hide"]();if((N.event.target===u.element[0]||N.event.target===u.get_container_ul()[0])&&u.get_container_ul().children().length===0){C=true;for(B=0,A=N.data.nodes.length;B<A;B++){C=C&&u.check((N.data.origin&&(N.data.origin.settings.dnd.always_copy||(N.data.origin.settings.dnd.copy&&(N.event.metaKey||N.event.ctrlKey)))?"copy_node":"move_node"),(N.data.origin&&N.data.origin!==u?N.data.origin.get_node(N.data.nodes[B]):N.data.nodes[B]),"#","last",{dnd:true,ref:u.get_node("#"),pos:"i",is_multi:(N.data.origin&&N.data.origin!==u),is_foreign:(!N.data.origin)});if(!C){break}}if(C){s={ins:u,par:"#",pos:"last"};p.hide();N.helper.find(".jstree-icon:eq(0)").removeClass("jstree-er").addClass("jstree-ok");return}}else{x=i(N.event.target).closest(".jstree-anchor");if(x&&x.length&&x.parent().is(".jstree-closed, .jstree-open, .jstree-leaf")){M=x.offset();v=N.event.pageY-M.top;K=x.height();if(v<K/3){F=["b","i","a"]}else{if(v>K-K/3){F=["a","i","b"]}else{F=v>K/2?["i","a","b"]:["i","b","a"]}}i.each(F,function(O,t){switch(t){case"b":I=M.left-6;D=M.top;E=u.get_parent(x);J=x.parent().index();break;case"i":y=u.settings.dnd.inside_pos;w=u.get_node(x.parent());I=M.left-2;D=M.top+K/2+1;E=w.id;J=y==="first"?0:(y==="last"?w.children.length:Math.min(y,w.children.length));break;case"a":I=M.left-6;D=M.top+K;E=u.get_parent(x);J=x.parent().index()+1;break}
+/*
+								// TODO: moving inside, but the node is not yet loaded?
+								// the check will work anyway, as when moving the node will be loaded first and checked again
+								if(v === 'i' && !ins.is_loaded(p)) { }
+								*/
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function(){P.open_node(Q)}}(u,x)),u.settings.dnd.open_timeout)}s={ins:u,par:E,pos:t==="i"&&y==="last"&&J===0&&!u.is_loaded(w)?"last":J};p.css({left:I+"px",top:D+"px"}).show();N.helper.find(".jstree-icon:eq(0)").removeClass("jstree-er").addClass("jstree-ok");r={};F=true;return false}});if(F===true){return}}}}s=false;N.helper.find(".jstree-icon").removeClass("jstree-ok").addClass("jstree-er");p.hide()}).bind("dnd_scroll.vakata",function(u,t){if(!t||!t.data||!t.data.jstree){return}p.hide();s=false;t.helper.find(".jstree-icon:eq(0)").removeClass("jstree-ok").addClass("jstree-er")}).bind("dnd_stop.vakata",function(x,w){if(q){clearTimeout(q)}if(!w||!w.data||!w.data.jstree){return}p.hide();var v,u,t=[];if(s){for(v=0,u=w.data.nodes.length;v<u;v++){t[v]=w.data.origin?w.data.origin.get_node(w.data.nodes[v]):w.data.nodes[v];if(w.data.origin){t[v].instance=w.data.origin}}s.ins[w.data.origin&&(w.data.origin.settings.dnd.always_copy||(w.data.origin.settings.dnd.copy&&(w.event.metaKey||w.event.ctrlKey)))?"copy_node":"move_node"](t,s.par,s.pos)}else{v=i(w.event.target).closest(".jstree");if(v.length&&r&&r.error&&r.error==="check"){v=v.jstree(true);if(v){v.settings.core.error.call(this,r)}}}}).bind("keyup keydown",function(u,t){t=i.vakata.dnd._get();if(t&&t.data&&t.data.jstree){t.helper.find(".jstree-copy:eq(0)")[t.data.origin&&(t.data.origin.settings.dnd.always_copy||(t.data.origin.settings.dnd.copy&&(u.metaKey||u.ctrlKey)))?"show":"hide"]()}})});(function(q){var p={element:false,target:false,is_down:false,is_drag:false,helper:false,helper_w:0,data:false,init_x:0,init_y:0,scroll_l:0,scroll_t:0,scroll_e:false,scroll_i:false,is_touch:false};q.vakata.dnd={settings:{scroll_speed:10,scroll_proximity:20,helper_left:5,helper_top:10,threshold:5,threshold_touch:50},_trigger:function(t,s){var r=q.vakata.dnd._get();r.event=s;q(document).triggerHandler("dnd_"+t+".vakata",r)},_get:function(){return{data:p.data,element:p.element,helper:p.helper}},_clean:function(){if(p.helper){p.helper.remove()}if(p.scroll_i){clearInterval(p.scroll_i);p.scroll_i=false}p={element:false,target:false,is_down:false,is_drag:false,helper:false,helper_w:0,data:false,init_x:0,init_y:0,scroll_l:0,scroll_t:0,scroll_e:false,scroll_i:false,is_touch:false};q(document).off("mousemove touchmove",q.vakata.dnd.drag);q(document).off("mouseup touchend",q.vakata.dnd.stop)},_scroll:function(t){if(!p.scroll_e||(!p.scroll_l&&!p.scroll_t)){if(p.scroll_i){clearInterval(p.scroll_i);p.scroll_i=false}return false}if(!p.scroll_i){p.scroll_i=setInterval(q.vakata.dnd._scroll,100);return false}if(t===true){return false}var s=p.scroll_e.scrollTop(),r=p.scroll_e.scrollLeft();p.scroll_e.scrollTop(s+p.scroll_t*q.vakata.dnd.settings.scroll_speed);p.scroll_e.scrollLeft(r+p.scroll_l*q.vakata.dnd.settings.scroll_speed);if(s!==p.scroll_e.scrollTop()||r!==p.scroll_e.scrollLeft()){q.vakata.dnd._trigger("scroll",p.scroll_e)}},start:function(t,s,r){if(t.type==="touchstart"&&t.originalEvent&&t.originalEvent.changedTouches&&t.originalEvent.changedTouches[0]){t.pageX=t.originalEvent.changedTouches[0].pageX;t.pageY=t.originalEvent.changedTouches[0].pageY;t.target=document.elementFromPoint(t.originalEvent.changedTouches[0].pageX-window.pageXOffset,t.originalEvent.changedTouches[0].pageY-window.pageYOffset)}if(p.is_drag){q.vakata.dnd.stop({})}try{t.currentTarget.unselectable="on";t.currentTarget.onselectstart=function(){return 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Preventing: "+A,data:JSON.stringify({chk:A,pos:B,obj:w&&w.id?w.id:false,par:x&&x.id?x.id:false})}}return v}return true};this.create_node=function(A,u,C,D,B){if(!u||u.text===e){if(A===null){A="#"}A=this.get_node(A);if(!A){return q.create_node.call(this,A,u,C,D,B)}C=C===e?"last":C;if(!C.toString().match(/^(before|after)$/)&&!B&&!this.is_loaded(A)){return q.create_node.call(this,A,u,C,D,B)}if(!u){u={}}var y,r,z,x,w,t=this._model.data,E=this.settings.unique.case_sensitive,v=this.settings.unique.duplicate;r=y=this.get_string("New node");z=[];for(x=0,w=A.children.length;x<w;x++){z.push(E?t[A.children[x]].text:t[A.children[x]].text.toLowerCase())}x=1;while(i.inArray(E?r:r.toLowerCase(),z)!==-1){r=v.call(this,y,(++x)).toString()}u.text=r}return q.create_node.call(this,A,u,C,D,B)}};var b=document.createElement("DIV");b.setAttribute("unselectable","on");b.className="jstree-wholerow";b.innerHTML=" ";i.jstree.plugins.wholerow=function(p,q){this.bind=function(){q.bind.call(this);this.element.on("ready.jstree set_state.jstree",i.proxy(function(){this.hide_dots()},this)).on("init.jstree loading.jstree ready.jstree",i.proxy(function(){this.get_container_ul().addClass("jstree-wholerow-ul")},this)).on("deselect_all.jstree",i.proxy(function(s,r){this.element.find(".jstree-wholerow-clicked").removeClass("jstree-wholerow-clicked")},this)).on("changed.jstree",i.proxy(function(v,u){this.element.find(".jstree-wholerow-clicked").removeClass("jstree-wholerow-clicked");var t=false,s,r;for(s=0,r=u.selected.length;s<r;s++){t=this.get_node(u.selected[s],true);if(t&&t.length){t.children(".jstree-wholerow").addClass("jstree-wholerow-clicked")}}},this)).on("open_node.jstree",i.proxy(function(s,r){this.get_node(r.node,true).find(".jstree-clicked").parent().children(".jstree-wholerow").addClass("jstree-wholerow-clicked")},this)).on("hover_node.jstree dehover_node.jstree",i.proxy(function(s,r){this.get_node(r.node,true).children(".jstree-wholerow")[s.type==="hover_node"?"addClass":"removeClass"]("jstree-wholerow-hovered")},this)).on("contextmenu.jstree",".jstree-wholerow",i.proxy(function(s){s.preventDefault();var r=i.Event("contextmenu",{metaKey:s.metaKey,ctrlKey:s.ctrlKey,altKey:s.altKey,shiftKey:s.shiftKey,pageX:s.pageX,pageY:s.pageY});i(s.currentTarget).closest(".jstree-node").children(".jstree-anchor:eq(0)").trigger(r)},this)).on("click.jstree",".jstree-wholerow",function(s){s.stopImmediatePropagation();var r=i.Event("click",{metaKey:s.metaKey,ctrlKey:s.ctrlKey,altKey:s.altKey,shiftKey:s.shiftKey});i(s.currentTarget).closest(".jstree-node").children(".jstree-anchor:eq(0)").trigger(r).focus()}).on("click.jstree",".jstree-leaf > .jstree-ocl",i.proxy(function(s){s.stopImmediatePropagation();var r=i.Event("click",{metaKey:s.metaKey,ctrlKey:s.ctrlKey,altKey:s.altKey,shiftKey:s.shiftKey});i(s.currentTarget).closest(".jstree-node").children(".jstree-anchor:eq(0)").trigger(r).focus()},this)).on("mouseover.jstree",".jstree-wholerow, .jstree-icon",i.proxy(function(r){r.stopImmediatePropagation();this.hover_node(r.currentTarget);return false},this)).on("mouseleave.jstree",".jstree-node",i.proxy(function(r){this.dehover_node(r.currentTarget)},this))};this.teardown=function(){if(this.settings.wholerow){this.element.find(".jstree-wholerow").remove()}q.teardown.call(this)};this.redraw_node=function(t,r,u){t=q.redraw_node.call(this,t,r,u);if(t){var s=b.cloneNode(true);if(i.inArray(t.id,this._data.core.selected)!==-1){s.className+=" jstree-wholerow-clicked"}t.insertBefore(s,t.childNodes[0])}return t}}}));
\ No newline at end of file


https://bitbucket.org/galaxy/galaxy-central/commits/a5b5351b4cf3/
Changeset:   a5b5351b4cf3
User:        martenson
Date:        2014-09-08 18:59:10+00:00
Summary:     attributions
Affected #:  2 files

diff -r ecf83c3a2d0383c74e30dca41b602854326c7ee7 -r a5b5351b4cf3bf74ccc841d7b8ffe9c859f5d03e lib/galaxy/util/dictobj.py
--- a/lib/galaxy/util/dictobj.py
+++ b/lib/galaxy/util/dictobj.py
@@ -2,6 +2,10 @@
 
 class DictionaryObject(object):
   """
+  Helper class written by William Grim - grimwm
+  Original repo: https://github.com/grimwm/py-dictobj
+  Thank you!
+  ************************
   A class that has all the functionality of a normal Python dictionary, except
   for the fact it is itself immutable.  It also has the added feature of
   being able to lookup values by using keys as attributes.

diff -r ecf83c3a2d0383c74e30dca41b602854326c7ee7 -r a5b5351b4cf3bf74ccc841d7b8ffe9c859f5d03e lib/galaxy/util/jstree.py
--- a/lib/galaxy/util/jstree.py
+++ b/lib/galaxy/util/jstree.py
@@ -8,6 +8,11 @@
 
 class Node(dictobj.DictionaryObject):
   """
+  Helper class written by William Grim - grimwm
+  Original repo: https://github.com/grimwm/py-jstree
+  Code adjusted according to the idea of Frank Blechschmidt - FraBle
+  Thank you!
+  ************************
   This class exists as a helper to the JSTree.  Its "jsonData" method can
   generate sub-tree JSON without putting the logic directly into the JSTree.
 


https://bitbucket.org/galaxy/galaxy-central/commits/a4a6834f4b2f/
Changeset:   a4a6834f4b2f
User:        martenson
Date:        2014-09-08 19:03:47+00:00
Summary:     more attributions
Affected #:  2 files

diff -r a5b5351b4cf3bf74ccc841d7b8ffe9c859f5d03e -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 lib/galaxy/util/dictobj.py
--- a/lib/galaxy/util/dictobj.py
+++ b/lib/galaxy/util/dictobj.py
@@ -2,6 +2,20 @@
 
 class DictionaryObject(object):
   """
+  Copyright 2012 "Grim Apps"
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
   Helper class written by William Grim - grimwm
   Original repo: https://github.com/grimwm/py-dictobj
   Thank you!

diff -r a5b5351b4cf3bf74ccc841d7b8ffe9c859f5d03e -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 lib/galaxy/util/jstree.py
--- a/lib/galaxy/util/jstree.py
+++ b/lib/galaxy/util/jstree.py
@@ -8,6 +8,20 @@
 
 class Node(dictobj.DictionaryObject):
   """
+  Copyright 2012 "Grim Apps"
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+   
   Helper class written by William Grim - grimwm
   Original repo: https://github.com/grimwm/py-jstree
   Code adjusted according to the idea of Frank Blechschmidt - FraBle


https://bitbucket.org/galaxy/galaxy-central/commits/858c12951cfa/
Changeset:   858c12951cfa
User:        martenson
Date:        2014-09-16 15:39:17+00:00
Summary:     allow admins to paste paths, pack scripts
Affected #:  6 files

diff -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 -r 858c12951cfa764fb8b948e360b29f8a9e90b89b lib/galaxy/webapps/galaxy/api/lda_datasets.py
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -435,22 +435,28 @@
         link_data = util.string_as_bool( kwd.get( 'link_data', False ) )
 
         source = kwd.get( 'source', None )
-        if source not in [ 'userdir_file', 'userdir_folder' ]:
-            raise exceptions.RequestParameterMissingException( 'You have to specify "source" parameter. Possible values are "userdir_file" and "userdir_folder". ')
+        if source not in [ 'userdir_file', 'userdir_folder', 'admin_path' ]:
+            raise exceptions.RequestParameterMissingException( 'You have to specify "source" parameter. Possible values are "userdir_file", "userdir_folder" and "admin_path". ')
 
-        user_login = trans.user.email
-        user_base_dir = trans.app.config.user_library_import_dir
-        if user_base_dir is None:
-            raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' )
-        full_dir = os.path.join( user_base_dir, user_login )
-        # path_to_root_import_folder = None
-        if not path.lower().startswith( full_dir.lower() ):
-            # path_to_root_import_folder = path
-            path = os.path.join( full_dir, path )
-        if not os.path.exists( path ):
-            raise exceptions.RequestParameterInvalidException( 'Given path does not exist on the host.' )
-        if not self.folder_manager.can_add_item( trans, folder ):
-            raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to add items to the given folder.' )
+        if source in [ 'userdir_file', 'userdir_folder' ]:
+            user_login = trans.user.email
+            user_base_dir = trans.app.config.user_library_import_dir
+            if user_base_dir is None:
+                raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' )
+            full_dir = os.path.join( user_base_dir, user_login )
+            # path_to_root_import_folder = None
+            if not path.lower().startswith( full_dir.lower() ):
+                # path_to_root_import_folder = path
+                path = os.path.join( full_dir, path )
+            if not os.path.exists( path ):
+                raise exceptions.RequestParameterInvalidException( 'Given path does not exist on the host.' )
+            if not self.folder_manager.can_add_item( trans, folder ):
+                raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to add items to the given folder.' )
+        if source == 'admin_path':
+            if not trans.app.config.allow_library_path_paste:
+                raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow admins to import into library from path.' )
+            if not trans.user_is_admin:
+                raise exceptions.AdminRequiredException( 'Only admins can import from path.' )
 
         # Set up the traditional tool state/params
         tool_id = 'upload1'
@@ -466,24 +472,32 @@
         abspath_datasets = []
         kwd[ 'filesystem_paths' ] = path
         params = util.Params( kwd )
-        # file only
+        # user wants to import one file only
         if source == "userdir_file":
             file = os.path.abspath( path )
             abspath_datasets.append( trans.webapp.controllers[ 'library_common' ].make_library_uploaded_dataset(
                 trans, 'api', params, os.path.basename( file ), file, 'server_dir', library_bunch ) )
-        # whole folder
+        # user wants to import whole folder
         if source == "userdir_folder":
             # import_folder_root = [next(part for part in path.split(os.path.sep) if part) for path in [os.path.splitdrive(path_to_root_import_folder)[1]]]
             # new_folder = self.folder_manager.create( trans, folder_id, import_folder_root[0] )
 
             uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( 
                 trans, 'api', params, library_bunch, 200, '' )
-
             uploaded_datasets = uploaded_datasets_bunch[0]
             if uploaded_datasets is None:
-                #  TODO no files found - only create folders
-                return False
-
+                raise exceptions.ObjectNotFound( 'Given folder does not contain any datasets.' )
+            for ud in uploaded_datasets:
+                ud.path = os.path.abspath( ud.path )
+                abspath_datasets.append( ud )
+        #  user wants to import from path (admins only)
+        if source == "admin_path":
+            # validate the path is within root
+            uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( 
+                trans, 'api', params, library_bunch, 200, '' )
+            uploaded_datasets = uploaded_datasets_bunch[0]
+            if uploaded_datasets is None:
+                raise exceptions.ObjectNotFound( 'Given folder does not contain any datasets.' )
             for ud in uploaded_datasets:
                 ud.path = os.path.abspath( ud.path )
                 abspath_datasets.append( ud )

diff -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 -r 858c12951cfa764fb8b948e360b29f8a9e90b89b static/scripts/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -199,10 +199,9 @@
   },
 
   /**
-   * import all selected datasets into history
+   * Import all selected datasets into history.
    */
   importAllIntoHistory : function (){
-      // disable the button to prevent multiple submission
       this.modal.disableButton('Import');
 
       // init the control counters
@@ -288,7 +287,11 @@
       $('.completion_span').text(txt_representation);
   },
 
-  // download selected datasets
+  /**
+   * download selected datasets
+   * @param  {str} folder_id id of the current folder
+   * @param  {str} format    requested archive format
+   */
   download : function(folder_id, format){
     var dataset_ids = [];
         $('#folder_table').find(':checked').each(function(){
@@ -296,29 +299,34 @@
                 dataset_ids.push(this.parentElement.parentElement.id);
             }
         });
-
     var url = '/api/libraries/datasets/download/' + format;
     var data = {'ldda_ids' : dataset_ids};
     this.processDownload(url, data, 'get');
   },
 
-  // create hidden form and submit through POST to initialize download
+  /**
+   * Create hidden form and submit it through POST
+   * to initialize the download.
+   * @param  {str} url    url to call
+   * @param  {obj} data   data to include in the request
+   * @param  {str} method method of the request
+   */
   processDownload: function(url, data, method){
-    //url and data options required
-    if( url && data ){
-            //data can be string of parameters or array/object
-            data = typeof data === 'string' ? data : $.param(data);
-            //split params into form inputs
-            var inputs = '';
-            $.each(data.split('&'), function(){
-                    var pair = this.split('=');
-                    inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
-            });
-            //send request
-            $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
-            .appendTo('body').submit().remove();
-            
-            mod_toastr.info('Your download will begin soon');
+    if ( url && data ){
+      // data can be string of parameters or array/object
+      data = typeof data === 'string' ? data : $.param(data);
+      // split params into form inputs
+      var inputs = '';
+      $.each(data.split('&'), function(){
+              var pair = this.split('=');
+              inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
+      });
+      // send request
+      $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
+      .appendTo('body').submit().remove();
+      mod_toastr.info('Your download will begin soon');
+    } else {
+      mod_toastr.error('An error occurred :(');
     }
   },
 
@@ -352,6 +360,33 @@
     });
   },
 
+  /**
+   * Create modal for importing from Galaxy path.
+   * This feature is admin-only.
+   */
+  importFilesFromPathModal: function(){
+    var that = this;
+    this.modal = Galaxy.modal;
+    var template_modal = this.templateImportPathModal();
+    this.modal.show({
+          closing_events  : true,
+          title           : 'Enter paths relative to Galaxy root',
+          body            : template_modal({}),
+          buttons         : {
+              'Import'    : function() {that.importFromPathsClicked(that);},
+              'Close'     : function() {Galaxy.modal.hide();}
+          },
+          closing_callback: function(){
+            //  TODO: should not trigger routes outside of the router
+            Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
+          }
+      });  
+  },
+
+  /**
+   * Create modal for importing form user's directory
+   * on Galaxy. Bind jQuery events.
+   */
   importFilesFromUserdirModal: function(){
     var that = this;
     this.modal = Galaxy.modal;
@@ -373,23 +408,28 @@
 
     $('input[type=radio]').change(function(event){
         if (event.target.value ==='jstree-disable-folders') {
+          that.renderJstree({disabled_jstree_element: 'folders'});
           $('.jstree-folders-message').hide();
           $('.jstree-preserve-structure').hide();
           $('.jstree-link-files').hide();
           $('.jstree-files-message').show();
-
-          that.renderJstree({disabled_jstree_element: 'folders'});
         } else if (event.target.value ==='jstree-disable-files'){
-          that.renderJstree({disabled_jstree_element: 'files'});
           $('.jstree-files-message').hide();
           $('.jstree-folders-message').show();
           $('.jstree-link-files').show();
           $('.jstree-preserve-structure').show();
+          that.renderJstree({disabled_jstree_element: 'files'});
         }
       }
     );     
   },
 
+  /**
+   * Fetch the contents of user directory on Galaxy
+   * and render jstree component based on received
+   * data.
+   * @param  {[type]} options [description]
+   */
   renderJstree: function(options){
     var that = this;
     this.options = _.extend(this.options, options);
@@ -427,13 +467,51 @@
     })
   },
 
-  importFoldersFromUserdir: function(){
-
+  /**
+   * Take the paths from the textarea, split it, create
+   * a request queue and call a function that starts sending
+   * one by one to be imported on the server.
+   */
+  importFromPathsClicked: function(){
+    var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
+    var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
+    var paths = $('textarea#import_paths').val();
+    if (!paths){
+      mod_toastr.info('Please enter a path relative to Galaxy root');
+    } else {
+      this.modal.disableButton('Import');
+      paths = paths.split('\n');
+      var valid_paths = [];
+      for (var i = paths.length - 1; i >= 0; i--) {
+        trimmed = paths[i].trim();
+        if (trimmed.length!==0){
+          valid_paths.push(trimmed);
+        }
+      };
+      this.initChainCallControl(valid_paths.length);
+      this.chainCallImportingFolders(valid_paths, preserve_dirs, link_data, 'admin_path');
+    }
   },
 
+  /**
+   * Initialize the control of chaining requests
+   * in the current modal.
+   */
+  initChainCallControl: function(length){
+    var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
+    this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
+    this.progress = 0;
+    this.progressStep = 100 / length;
+    this.options.chain_call_control.total_number = length;
+    this.options.chain_call_control.failed_number = 0;
+  },
 
-  // add all selected datasets from user directory into current folder
-  importFromUserdirClicked : function (that){
+  /**
+   * Take the selected items from the jstree, create a request queue
+   * and send them one by one to the server for importing into 
+   * the current folder.
+   */
+  importFromUserdirClicked: function (that){
     var selected_nodes = $('#jstree_browser').jstree().get_selected(true);
     var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
     var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
@@ -443,7 +521,7 @@
     } else {
       // disable the button to prevent multiple submission
       this.modal.disableButton('Import');
-      // init the control counters
+      // init the chain control counters
       this.options.chain_call_control.total_number = 0;
       this.options.chain_call_control.failed_number = 0;
 
@@ -452,9 +530,8 @@
           paths.push(selected_nodes[i].li_attr.full_path);
         }
       }
-      var folder_name = this.options.folder_name;
       var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-      this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : folder_name }));
+      this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
 
       // init the progress bar
       this.progressStep = 100 / paths.length;
@@ -464,13 +541,18 @@
       var selection_type = selected_nodes[0].type;
       // call the recursive function to call ajax one after each other (request FIFO queue)
       if (selection_type === 'folder'){
-        this.chainCallImportingUserdirFolders(paths, preserve_dirs, link_data);
+        this.chainCallImportingFolders(paths, preserve_dirs, link_data, 'userdir_folder');
       } else if (selection_type === 'file'){
         this.chainCallImportingUserdirFiles(paths);
       }
     }
   },
 
+  /**
+   * Take the array of paths and createa request for each of them
+   * calling them in chain. Update the progress bar in between each.
+   * @param  {array} paths           paths relative to user folder on Galaxy
+   */
   chainCallImportingUserdirFiles: function(paths){
     var that = this;
     var popped_item = paths.pop();
@@ -483,21 +565,30 @@
       }
       return true;
     }
-    var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id + '&source=userdir_file&path=' + popped_item))
+    var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id + 
+                                                       '&source=userdir_file' +
+                                                       '&path=' + popped_item))
     promise.done(function(response){
-              // we are fine
               that.updateProgress();
               that.chainCallImportingUserdirFiles(paths);
             })
             .fail(function(){
-              // we have a problem
               that.options.chain_call_control.failed_number += 1;
               that.updateProgress();
               that.chainCallImportingUserdirFiles(paths);
             });
   },
 
-  chainCallImportingUserdirFolders: function(paths, preserve_dirs, link_data){
+  /**
+   * Take the array of paths and createa request for each of them
+   * calling them in chain. Update the progress bar in between each.
+   * @param  {array} paths           paths relative to Galaxy root folder
+   * @param  {boolean} preserve_dirs indicates whether to preserve folder structure
+   * @param  {boolean} link_data     copy files to Galaxy or link instead
+   * @param  {str} source            string representing what type of folder 
+   *                                 is the source of import
+   */
+  chainCallImportingFolders: function(paths, preserve_dirs, link_data, source){
     // need to check which paths to call
     var that = this;
     var popped_item = paths.pop();
@@ -508,23 +599,20 @@
       } else {
         mod_toastr.error('Something went wrong :(');
       }
-      return true;
     }
     var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
-                                                      '&source=userdir_folder' +
+                                                      '&source=' + source +
                                                       '&path=' + popped_item +
                                                       '&preserve_dirs=' + preserve_dirs +
-                                                      '&link_data=' + link_data ))
+                                                      '&link_data=' + link_data))
     promise.done(function(response){
-              // we are fine
               that.updateProgress();
-              that.chainCallImportingUserdirFolders(paths);
+              that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
             })
             .fail(function(){
-              // we have a problem
               that.options.chain_call_control.failed_number += 1;
               that.updateProgress();
-              that.chainCallImportingUserdirFolders(paths);
+              that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
             });
   },
 
@@ -566,9 +654,8 @@
                 history_dataset_ids.push(hid);
             }
         });
-        var folder_name = this.options.folder_name;
         var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-        this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : folder_name }));
+        this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
 
         // init the progress bar
         this.progressStep = 100 / history_dataset_ids.length;
@@ -759,7 +846,7 @@
       case "importdir":
         break;
       case "path": 
-        mod_toastr.info('Coming soon.');
+        this.importFilesFromPathModal();
         break;
       case "userdir":
         this.importFilesFromUserdirModal();
@@ -961,6 +1048,30 @@
     return _.template(tmpl_array.join(''));
   },
 
+  templateImportPathModal: function(){
+    var tmpl_array = [];
+
+    tmpl_array.push('<div id="file_browser_modal">');
+
+    tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure">');
+    tmpl_array.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
+    tmpl_array.push('Preserve directory structure');
+    tmpl_array.push(' </label>');
+
+    tmpl_array.push('<label class="checkbox-inline jstree-link-files">');
+    tmpl_array.push('   <input class="link-checkbox" type="checkbox" value="link_files">');
+    tmpl_array.push('Link files instead of copying');
+    tmpl_array.push(' </label>');
+    tmpl_array.push('</div>');
+
+    tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+
+    tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');
+    tmpl_array.push('</div>');
+
+    return _.template(tmpl_array.join(''));
+  },
+
   templateAddFilesFromHistory: function (){
     var tmpl_array = [];
 

diff -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 -r 858c12951cfa764fb8b948e360b29f8a9e90b89b static/scripts/packed/galaxy.library.js
--- a/static/scripts/packed/galaxy.library.js
+++ b/static/scripts/packed/galaxy.library.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_version",function(q,p,r){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,ldda_id:r,show_version:true})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download","folders/:folder_id/import/:source":"import_datasets"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_version",function(q,p,r){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,ldda_id:r,show_version:true})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});this.library_router.on("route:import_datasets",function(p,q){if(Galaxy.libraries.folderToolbarView&&Galaxy.libraries.folderListView){Galaxy.libraries.folderToolbarView.showImportModal({source:q})}else{Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p});Galaxy.libraries.folderToolbarView.showImportModal({source:q})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}});
\ No newline at end of file

diff -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 -r 858c12951cfa764fb8b948e360b29f8a9e90b89b static/scripts/packed/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(h){h.preventDefault();h.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var j=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=j;var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var k=100/o.length;this.initProgress(k);var f=[];for(var g=o.length-1;g>=0;g--){var h=o[g];var l=new c.HistoryItem();l.url=l.urlRoot+j+"/contents";l.content=h;l.source="library";f.push(l)}this.options.chain_call_control.total_number=f.length;jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+historyId);this.chainCall(f,m)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();var h=f.options.full_path[f.options.full_path.length-1][1];f.modal.show({closing_events:true,title:"Add datasets from history to "+h,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(i){f.fetchAndDisplayHistoryContents(i.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},showLibInfo:function(){var g=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var f=null;var h=this;if(Galaxy.libraries.libraryListView!==null){f=Galaxy.libraries.libraryListView.collection.get(g)}else{f=new c.Library({id:g});f.fetch({success:function(){var i=h.templateLibInfoInModal();h.modal=Galaxy.modal;h.modal.show({closing_events:true,title:"Library Information",body:i({library:f}),buttons:{Close:function(){Galaxy.modal.hide()}}})},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push("       <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push('   <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push('     <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push('     <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("   </div>");tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push('        <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push('        <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push("   <% _.each(histories, function(history) { %>");f.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push("   <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push('       <span class="completion_span">0% Complete</span>');f.push("   </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push('       <span class="completion_span">0% Complete</span>');f.push("   </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push('   <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push('       <span class="completion_span">0% Complete</span>');f.push("   </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history:  ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push("   <% _.each(histories, function(history) { %>");f.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push("   <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push('   <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","libs/jquery/jstree","mvc/library/library-model"],function(c,e,f,b,d){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}else{f.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var g=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new d.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";g.push(m)}this.options.chain_call_control.total_number=g.length;jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCall(g,n)},chainCall:function(h,k){var g=this;var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCall(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCall(h,k)})},initProgress:function(g){this.progress=0;this.progressStep=g},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon")}else{f.error("An error occurred :(")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred :(")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Enter paths relative to Galaxy root",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Select folders or files to import",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){$("#jstree_browser").jstree("destroy");var l=$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var l=this.modal.$el.find(".link-checkbox").is(":checked");var k=$("textarea#import_paths").val();if(!k){f.info("Please enter a path relative to Galaxy root")}else{this.modal.disableButton("Import");k=k.split("\n");var j=[];for(var h=k.length-1;h>=0;h--){trimmed=k[h].trim();if(trimmed.length!==0){j.push(trimmed)}}this.initChainCallControl(j.length);this.chainCallImportingFolders(j,g,l,"admin_path")}},initChainCallControl:function(g){var h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));this.progress=0;this.progressStep=100/g;this.options.chain_call_control.total_number=g;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(l){var h=$("#jstree_browser").jstree().get_selected(true);var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var n=[];if(h.length<1){f.info("You have to select some items first")}else{this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;for(var j=h.length-1;j>=0;j--){if(h[j].li_attr.full_path!==undefined){n.push(h[j].li_attr.full_path)}}var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/n.length;this.progress=0;this.options.chain_call_control.total_number=n.length;var k=h[0].type;if(k==="folder"){this.chainCallImportingFolders(n,g,o,"userdir_folder")}else{if(k==="file"){this.chainCallImportingUserdirFiles(n)}}}},chainCallImportingUserdirFiles:function(j){var g=this;var h=j.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}return true}var i=$.when($.post("/api/libraries/datasets?encoded_folder_id="+g.id+"&source=userdir_file&path="+h));i.done(function(k){g.updateProgress();g.chainCallImportingUserdirFiles(j)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingUserdirFiles(j)})},chainCallImportingFolders:function(l,g,m,j){var h=this;var i=l.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}}var k=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+j+"&path="+i+"&preserve_dirs="+g+"&link_data="+m));k.done(function(n){h.updateProgress();h.chainCallImportingFolders(l,g,m,j)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(l,g,m,j)})},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");if(l.length<1){f.info("You have to select some datasets first")}else{this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/g.length;this.progress=0;var k=[];for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.options.chain_call_control.total_number=k.length;this.chainCallAddingHdas(k)}},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push("   <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push('   <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li class="divider"></li>');tmpl_array.push('        <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push("<% } else { %>");tmpl_array.push('     <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div id="jstree_browser">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history:  ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push('   <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file

diff -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 -r 858c12951cfa764fb8b948e360b29f8a9e90b89b static/scripts/packed/mvc/library/library-libraryrow-view.js
--- a/static/scripts/packed/mvc/library/library-libraryrow-view.js
+++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove()},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.repaint(g);e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push('           <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push("               <% if(!edit_mode) { %>");tmpl_array.push('                 <% if(library.get("deleted")) { %>');tmpl_array.push('                   <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push("                 <% } else { %>");tmpl_array.push('                   <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push("                 <% } %>");tmpl_array.push('                 <% if(library.get("description")) { %>');tmpl_array.push('                   <% if( (library.get("description")).length> 80 ) { %>');tmpl_array.push('                     <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>');tmpl_array.push("                   <% } else { %>");tmpl_array.push('                     <td><%= _.escape(library.get("description"))%></td>');tmpl_array.push("                   <% } %>");tmpl_array.push("                 <% } else { %>");tmpl_array.push("                   <td></td>");tmpl_array.push("                 <% } %>");tmpl_array.push('                 <% if(library.get("synopsis")) { %>');tmpl_array.push('                   <% if( (library.get("synopsis")).length> 120 ) { %>');tmpl_array.push('                     <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>');tmpl_array.push("                   <% } else { %>");tmpl_array.push('                     <td><%= _.escape(library.get("synopsis"))%></td>');tmpl_array.push("                   <% } %>");tmpl_array.push("                 <% } else { %>");tmpl_array.push("                   <td></td>");tmpl_array.push("                 <% } %>");tmpl_array.push("               <% } else if(edit_mode){ %>");tmpl_array.push('                 <td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>');tmpl_array.push('                 <td><textarea rows="4"  class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>');tmpl_array.push('                 <td><textarea rows="4"  class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>');tmpl_array.push("               <% } %>");tmpl_array.push('               <td class="right-center">');tmpl_array.push('                   <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push('                     <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push("                   <% }%>");tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push('                   <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push("               </td>");tmpl_array.push("           </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.repaint(g);e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push('           <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push("               <% if(!edit_mode) { %>");tmpl_array.push('                 <% if(library.get("deleted")) { %>');tmpl_array.push('                   <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push("                 <% } else { %>");tmpl_array.push('                   <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push("                 <% } %>");tmpl_array.push('                 <% if(library.get("description")) { %>');tmpl_array.push('                   <% if( (library.get("description")).length> 80 ) { %>');tmpl_array.push('                     <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>');tmpl_array.push("                   <% } else { %>");tmpl_array.push('                     <td><%= _.escape(library.get("description"))%></td>');tmpl_array.push("                   <% } %>");tmpl_array.push("                 <% } else { %>");tmpl_array.push("                   <td></td>");tmpl_array.push("                 <% } %>");tmpl_array.push('                 <% if(library.get("synopsis")) { %>');tmpl_array.push('                   <% if( (library.get("synopsis")).length> 120 ) { %>');tmpl_array.push('                     <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>');tmpl_array.push("                   <% } else { %>");tmpl_array.push('                     <td><%= _.escape(library.get("synopsis"))%></td>');tmpl_array.push("                   <% } %>");tmpl_array.push("                 <% } else { %>");tmpl_array.push("                   <td></td>");tmpl_array.push("                 <% } %>");tmpl_array.push("               <% } else if(edit_mode){ %>");tmpl_array.push('                 <td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>');tmpl_array.push('                 <td><textarea rows="4"  class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>');tmpl_array.push('                 <td><textarea rows="4"  class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>');tmpl_array.push("               <% } %>");tmpl_array.push('               <td class="right-center">');tmpl_array.push('                   <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push('                     <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push("                   <% }%>");tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push('                   <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push('                   <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push("               </td>");tmpl_array.push("           </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}});
\ No newline at end of file

diff -r a4a6834f4b2fe443f40235fd6331a7da7fa09d57 -r 858c12951cfa764fb8b948e360b29f8a9e90b89b static/scripts/packed/mvc/library/library-model.js
--- a/static/scripts/packed/mvc/library/library-model.js
+++ b/static/scripts/packed/mvc/library/library-model.js
@@ -1,1 +1,1 @@
-define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(m){var l=true;if((!m)&&(this.get("deleted"))){l=false}return l}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(l){l=l||{}},getVisible:function(m,n){n=n||[];var l=new i(this.filter(function(o){return o.isVisible(m)}));return l},sortByNameAsc:function(){this.comparator=function(m,l){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(m,l){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var k=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(m,l){if(m.get("type")===l.get("type")){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}return 0}else{if(m.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(m,l){if(m.get("type")===l.get("type")){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}return 0}else{if(m.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(l){this.get("folder").reset(l.folder_contents);return l}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(l){this.id=l.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Ldda:k,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}});
\ No newline at end of file
+define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(n){var m=true;if((!n)&&(this.get("deleted"))){m=false}return m}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(m){m=m||{}},getVisible:function(n,o){o=o||[];var m=new i(this.filter(function(p){return p.isVisible(n)}));return m},sortByNameAsc:function(){this.comparator=function(n,m){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(n,m){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var l=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(n,m){if(n.get("type")===m.get("type")){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return -1}return 0}else{if(n.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(n,m){if(n.get("type")===m.get("type")){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return 1}return 0}else{if(n.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(m){this.get("folder").reset(m.folder_contents);return m}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(m){this.id=m.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var k=Backbone.Collection.extend({url:"/api/histories",model:h});var j=Backbone.Model.extend({urlRoot:"/api/ftp_files"});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Ldda:l,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:k,Jstree:j}});
\ No newline at end of file


https://bitbucket.org/galaxy/galaxy-central/commits/d277478dce50/
Changeset:   d277478dce50
User:        martenson
Date:        2014-09-16 15:40:08+00:00
Summary:     Merge
Affected #:  293 files

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 config/plugins/visualizations/charts/templates/charts.mako
--- a/config/plugins/visualizations/charts/templates/charts.mako
+++ b/config/plugins/visualizations/charts/templates/charts.mako
@@ -86,8 +86,8 @@
                 require(['plugin/app'], function(App) {
                     // load options
                     var options = {
-                        id      : ${h.to_json_string( visualization_id )} || undefined,
-                        config  : ${h.to_json_string( config )}
+                        id      : ${h.dumps( visualization_id )} || undefined,
+                        config  : ${h.dumps( config )}
                     }
                     
                     // create application

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 config/plugins/visualizations/common/templates/config_utils.mako
--- a/config/plugins/visualizations/common/templates/config_utils.mako
+++ b/config/plugins/visualizations/common/templates/config_utils.mako
@@ -36,7 +36,7 @@
         'action'        : 'saved',
         'type'          : visualization_name,
         'title'         : title,
-        'config'        : h.to_json_string( config )
+        'config'        : h.dumps( config )
     }
     # save to existing visualization
     if visualization_id:

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 config/plugins/visualizations/scatterplot/templates/scatterplot.mako
--- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako
+++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako
@@ -50,11 +50,11 @@
 <script type="text/javascript">
 $(function(){
     var model = new ScatterplotModel({
-            id      : ${h.to_json_string( visualization_id )} || undefined,
+            id      : ${h.dumps( visualization_id )} || undefined,
             title   : "${title}",
-            config  : ${h.to_json_string( config, indent=2 )}
+            config  : ${h.dumps( config, indent=2 )}
         });
-        hdaJson = ${h.to_json_string( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )},
+        hdaJson = ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )},
         display = new ScatterplotDisplay({
             el      : $( '.scatterplot-display' ).attr( 'id', 'scatterplot-display-' + '${visualization_id}' ),
             model   : model,
@@ -78,11 +78,11 @@
 <script type="text/javascript">
 $(function(){
     var model   = new ScatterplotModel({
-            id      : ${h.to_json_string( visualization_id )} || undefined,
+            id      : ${h.dumps( visualization_id )} || undefined,
             title   : "${title or default_title}",
-            config  : ${h.to_json_string( config, indent=2 )}
+            config  : ${h.dumps( config, indent=2 )}
         }),
-        hdaJson = ${h.to_json_string( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )},
+        hdaJson = ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )},
         editor  = new ScatterplotConfigEditor({
             el      : $( '.scatterplot-editor' ).attr( 'id', 'scatterplot-editor-hda-' + hdaJson.id ),
             model   : model,

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/igv/bam.xml
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -12,15 +12,19 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
-        <filter>${dataset.dbkey in $site_dbkeys}</filter>
-        
+        <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>
+
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${redirect_url}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><param type="template" name="site_organism" strip="True" >
-            $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
+            #if ($dataset.dbkey in $site_dbkeys)
+                $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
+            #else:
+                $bam_file.dbkey
+            #end if
         </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/igv/vcf.xml
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -12,15 +12,19 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
-        <filter>${dataset.dbkey in $site_dbkeys}</filter>
-        
+        <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>
+
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${redirect_url}</url><param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /><param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /><param type="template" name="site_organism" strip="True" >
-            $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ]
+            #if ($dataset.dbkey in $site_dbkeys)
+                $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ]
+            #else:
+                $bgzip_file.dbkey
+            #end if
         </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/ucsc/bam.xml
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/><dynamic_param name="builds" value="2" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter><filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/ucsc/bigbed.xml
--- a/display_applications/ucsc/bigbed.xml
+++ b/display_applications/ucsc/bigbed.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/><dynamic_param name="builds" value="2" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter><filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bigbed_file.dbkey)}&hgt.customText=${qp($track.url)}</url>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/ucsc/bigwig.xml
--- a/display_applications/ucsc/bigwig.xml
+++ b/display_applications/ucsc/bigwig.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/><dynamic_param name="builds" value="2" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter><filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bigwig_file.dbkey)}&hgt.customText=${qp($track.url)}</url>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/ucsc/interval_as_bed.xml
--- a/display_applications/ucsc/interval_as_bed.xml
+++ b/display_applications/ucsc/interval_as_bed.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/><dynamic_param name="builds" value="2" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter><filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp}</url>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/ucsc/maf_customtrack.xml
--- a/display_applications/ucsc/maf_customtrack.xml
+++ b/display_applications/ucsc/maf_customtrack.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/><dynamic_param name="builds" value="2" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter><filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($maf_customtrack_file.dbkey)}&position=${maf_customtrack_file.metadata.vp_chromosome}:${maf_customtrack_file.metadata.vp_start}-${maf_customtrack_file.metadata.vp_end}&hgt.customText=${maf_customtrack_file.qp}</url>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 display_applications/ucsc/vcf.xml
--- a/display_applications/ucsc/vcf.xml
+++ b/display_applications/ucsc/vcf.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/><dynamic_param name="builds" value="2" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter><filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bgzip_file.dbkey)}&hgt.customText=${qp($track.url)}</url>

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -5,7 +5,7 @@
 from galaxy import config, jobs
 import galaxy.model
 import galaxy.security
-from galaxy import dataset_collections
+from galaxy.managers.collections import DatasetCollectionManager
 import galaxy.quota
 from galaxy.tags.tag_handler import GalaxyTagHandler
 from galaxy.visualization.genomes import Genomes
@@ -57,7 +57,7 @@
         # Tag handler
         self.tag_handler = GalaxyTagHandler()
         # Dataset Collection Plugins
-        self.dataset_collections_service = dataset_collections.DatasetCollectionsService(self)
+        self.dataset_collections_service = DatasetCollectionManager(self)
 
         # Tool Data Tables
         self._configure_tool_data_tables( from_shed_config=False )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/dataset_collections/__init__.py
--- a/lib/galaxy/dataset_collections/__init__.py
+++ b/lib/galaxy/dataset_collections/__init__.py
@@ -1,295 +0,0 @@
-from .registry import DatasetCollectionTypesRegistry
-from .matching import MatchingCollections
-from .type_description import CollectionTypeDescriptionFactory
-
-
-from galaxy import model
-from galaxy.exceptions import MessageException
-from galaxy.exceptions import ItemAccessibilityException
-from galaxy.exceptions import RequestParameterInvalidException
-from galaxy.web.base.controller import (
-    UsesHistoryDatasetAssociationMixin,
-    UsesLibraryMixinItems,
-    UsesTagsMixin,
-)
-from galaxy.managers import hdas  # TODO: Refactor all mixin use into managers.
-from galaxy.managers.collections_util import validate_input_element_identifiers
-from galaxy.util import validation
-from galaxy.util import odict
-
-import logging
-log = logging.getLogger( __name__ )
-
-
-ERROR_INVALID_ELEMENTS_SPECIFICATION = "Create called with invalid parameters, must specify element identifiers."
-ERROR_NO_COLLECTION_TYPE = "Create called without specifing a collection type."
-
-
-class DatasetCollectionsService(
-    UsesHistoryDatasetAssociationMixin,
-    UsesLibraryMixinItems,
-    UsesTagsMixin,
-):
-    """
-    Abstraction for interfacing with dataset collections instance - ideally abstarcts
-    out model and plugin details.
-    """
-
-    def __init__( self, app ):
-        self.type_registry = DatasetCollectionTypesRegistry( app )
-        self.collection_type_descriptions = CollectionTypeDescriptionFactory( self.type_registry )
-        self.model = app.model
-        self.security = app.security
-        self.hda_manager = hdas.HDAManager()
-
-    def create(
-        self,
-        trans,
-        parent,  # PRECONDITION: security checks on ability to add to parent occurred during load.
-        name,
-        collection_type,
-        element_identifiers=None,
-        elements=None,
-        implicit_collection_info=None,
-    ):
-        """
-        """
-        # Trust embedded, newly created objects created by tool subsystem.
-        trusted_identifiers = implicit_collection_info is not None
-
-        if element_identifiers and not trusted_identifiers:
-            validate_input_element_identifiers( element_identifiers )
-
-        dataset_collection = self.__create_dataset_collection(
-            trans=trans,
-            collection_type=collection_type,
-            element_identifiers=element_identifiers,
-            elements=elements,
-        )
-        if isinstance( parent, model.History ):
-            dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
-                collection=dataset_collection,
-                name=name,
-            )
-            if implicit_collection_info:
-                for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]:
-                    dataset_collection_instance.add_implicit_input_collection( input_name, input_collection )
-                for output_dataset in implicit_collection_info.get( "outputs" ):
-                    output_dataset.hidden_beneath_collection_instance = dataset_collection_instance
-                    trans.sa_session.add( output_dataset )
-
-                dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ]
-            log.debug("Created collection with %d elements" % ( len( dataset_collection_instance.collection.elements ) ) )
-            # Handle setting hid
-            parent.add_dataset_collection( dataset_collection_instance )
-        elif isinstance( parent, model.LibraryFolder ):
-            dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation(
-                collection=dataset_collection,
-                folder=parent,
-                name=name,
-            )
-        else:
-            message = "Internal logic error - create called with unknown parent type %s" % type( parent )
-            log.exception( message )
-            raise MessageException( message )
-
-        return self.__persist( dataset_collection_instance )
-
-    def __create_dataset_collection(
-        self,
-        trans,
-        collection_type,
-        element_identifiers=None,
-        elements=None,
-    ):
-        if element_identifiers is None and elements is None:
-            raise RequestParameterInvalidException( ERROR_INVALID_ELEMENTS_SPECIFICATION )
-        if not collection_type:
-            raise RequestParameterInvalidException( ERROR_NO_COLLECTION_TYPE )
-        collection_type_description = self.collection_type_descriptions.for_collection_type( collection_type )
-        # If we have elements, this is an internal request, don't need to load
-        # objects from identifiers.
-        if elements is None:
-            if collection_type_description.has_subcollections( ):
-                # Nested collection - recursively create collections and update identifiers.
-                self.__recursively_create_collections( trans, element_identifiers )
-            elements = self.__load_elements( trans, element_identifiers )
-        # else if elements is set, it better be an ordered dict!
-
-        type_plugin = collection_type_description.rank_type_plugin()
-        dataset_collection = type_plugin.build_collection( elements )
-        dataset_collection.collection_type = collection_type
-        return dataset_collection
-
-    def delete( self, trans, instance_type, id ):
-        dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True )
-        dataset_collection_instance.deleted = True
-        trans.sa_session.add( dataset_collection_instance )
-        trans.sa_session.flush( )
-
-    def update( self, trans, instance_type, id, payload ):
-        dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True )
-        if trans.user is None:
-            anon_allowed_payload = {}
-            if 'deleted' in payload:
-                anon_allowed_payload[ 'deleted' ] = payload[ 'deleted' ]
-            if 'visible' in payload:
-                anon_allowed_payload[ 'visible' ] = payload[ 'visible' ]
-            payload = self._validate_and_parse_update_payload( anon_allowed_payload )
-        else:
-            payload = self._validate_and_parse_update_payload( payload )
-        changed = self._set_from_dict( trans, dataset_collection_instance, payload )
-        return changed
-
-    def copy(
-        self,
-        trans,
-        parent,  # PRECONDITION: security checks on ability to add to parent occurred during load.
-        source,
-        encoded_source_id,
-    ):
-        assert source == "hdca"  # for now
-        source_hdca = self.__get_history_collection_instance( trans, encoded_source_id )
-        new_hdca = source_hdca.copy()
-        parent.add_dataset_collection( new_hdca )
-        trans.sa_session.add( new_hdca )
-        trans.sa_session.flush()
-        return source_hdca
-
-    def _set_from_dict( self, trans, dataset_collection_instance, new_data ):
-        # Blatantly stolen from UsesHistoryDatasetAssociationMixin.set_hda_from_dict.
-
-        # send what we can down into the model
-        changed = dataset_collection_instance.set_from_dict( new_data )
-        # the rest (often involving the trans) - do here
-        if 'annotation' in new_data.keys() and trans.get_user():
-            dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] )
-            changed[ 'annotation' ] = new_data[ 'annotation' ]
-        if 'tags' in new_data.keys() and trans.get_user():
-            self.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user )
-
-        if changed.keys():
-            trans.sa_session.flush()
-
-        return changed
-
-    def _validate_and_parse_update_payload( self, payload ):
-        validated_payload = {}
-        for key, val in payload.items():
-            if val is None:
-                continue
-            if key in ( 'name' ):
-                val = validation.validate_and_sanitize_basestring( key, val )
-                validated_payload[ key ] = val
-            if key in ( 'deleted', 'visible' ):
-                validated_payload[ key ] = validation.validate_boolean( key, val )
-            elif key == 'tags':
-                validated_payload[ key ] = validation.validate_and_sanitize_basestring_list( key, val )
-        return validated_payload
-
-    def history_dataset_collections(self, history, query):
-        collections = history.active_dataset_collections
-        collections = filter( query.direct_match, collections )
-        return collections
-
-    def __persist( self, dataset_collection_instance ):
-        context = self.model.context
-        context.add( dataset_collection_instance )
-        context.flush()
-        return dataset_collection_instance
-
-    def __recursively_create_collections( self, trans, element_identifiers ):
-        for index, element_identifier in enumerate( element_identifiers ):
-            try:
-                if not element_identifier[ "src" ] == "new_collection":
-                    # not a new collection, keep moving...
-                    continue
-            except KeyError:
-                # Not a dictionary, just an id of an HDA - move along.
-                continue
-
-            # element identifier is a dict with src new_collection...
-            collection_type = element_identifier.get( "collection_type", None )
-            collection = self.__create_dataset_collection(
-                trans=trans,
-                collection_type=collection_type,
-                element_identifiers=element_identifier[ "element_identifiers" ],
-            )
-            element_identifier[ "__object__" ] = collection
-
-        return element_identifiers
-
-    def __load_elements( self, trans, element_identifiers ):
-        elements = odict.odict()
-        for element_identifier in element_identifiers:
-            elements[ element_identifier[ "name" ] ] = self.__load_element( trans, element_identifier )
-        return elements
-
-    def __load_element( self, trans, element_identifier ):
-        #if not isinstance( element_identifier, dict ):
-        #    # Is allowing this to just be the id of an hda too clever? Somewhat
-        #    # consistent with other API methods though.
-        #    element_identifier = dict( src='hda', id=str( element_identifier ) )
-
-        # Previously created collection already found in request, just pass
-        # through as is.
-        if "__object__" in element_identifier:
-            return element_identifier[ "__object__" ]
-
-        # dateset_identifier is dict {src=hda|ldda|hdca|new_collection, id=<encoded_id>}
-        try:
-            src_type = element_identifier.get( 'src', 'hda' )
-        except AttributeError:
-            raise MessageException( "Dataset collection element definition (%s) not dictionary-like." % element_identifier )
-        encoded_id = element_identifier.get( 'id', None )
-        if not src_type or not encoded_id:
-            raise RequestParameterInvalidException( "Problem decoding element identifier %s" % element_identifier )
-
-        if src_type == 'hda':
-            decoded_id = int( trans.app.security.decode_id( encoded_id ) )
-            element = self.hda_manager.get( trans, decoded_id, check_ownership=False )
-        elif src_type == 'ldda':
-            element = self.get_library_dataset_dataset_association( trans, encoded_id )
-        elif src_type == 'hdca':
-            # TODO: Option to copy? Force copy? Copy or allow if not owned?
-            element = self.__get_history_collection_instance( trans, encoded_id ).collection
-        # TODO: ldca.
-        else:
-            raise RequestParameterInvalidException( "Unknown src_type parameter supplied '%s'." % src_type )
-        return element
-
-    def match_collections( self, collections_to_match ):
-        """
-        May seem odd to place it here, but planning to grow sophistication and
-        get plugin types involved so it will likely make sense in the future.
-        """
-        return MatchingCollections.for_collections( collections_to_match, self.collection_type_descriptions )
-
-    def get_dataset_collection_instance( self, trans, instance_type, id, **kwds ):
-        """
-        """
-        if instance_type == "history":
-            return self.__get_history_collection_instance( trans, id, **kwds )
-        elif instance_type == "library":
-            return self.__get_library_collection_instance( trans, id, **kwds )
-
-    def get_dataset_collection( self, trans, encoded_id ):
-        collection_id = int( trans.app.security.decode_id( encoded_id ) )
-        collection = trans.sa_session.query( trans.app.model.DatasetCollection ).get( collection_id )
-        return collection
-
-    def __get_history_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ):
-        instance_id = int( trans.app.security.decode_id( id ) )
-        collection_instance = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( instance_id )
-        self.security_check( trans, collection_instance.history, check_ownership=check_ownership, check_accessible=check_accessible )
-        return collection_instance
-
-    def __get_library_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ):
-        if check_ownership:
-            raise NotImplemented( "Functionality (getting library dataset collection with ownership check) unimplemented." )
-        instance_id = int( trans.security.decode_id( id ) )
-        collection_instance = trans.sa_session.query( trans.app.model.LibraryDatasetCollectionAssociation ).get( instance_id )
-        if check_accessible:
-            if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), collection_instance, trans.user ):
-                raise ItemAccessibilityException( "LibraryDatasetCollectionAssociation is not accessible to the current user", type='error' )
-        return collection_instance

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
@@ -52,4 +52,4 @@
     FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/converters/fasta_to_len.py
--- a/lib/galaxy/datatypes/converters/fasta_to_len.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.py
@@ -49,4 +49,4 @@
     out.close()
 
 if __name__ == "__main__" :
-    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True )
\ No newline at end of file
+    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
@@ -40,4 +40,4 @@
         print >> out, "%s\t%s" %( fasta_title, sequence )
     out.close()
 
-if __name__ == "__main__" : __main__()
\ No newline at end of file
+if __name__ == "__main__" : __main__()

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
@@ -52,4 +52,4 @@
 
     outfile.close()
 
-if __name__ == "__main__": __main__()
\ No newline at end of file
+if __name__ == "__main__": __main__()

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/converters/interval_to_coverage.py
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.py
+++ b/lib/galaxy/datatypes/converters/interval_to_coverage.py
@@ -149,4 +149,4 @@
                                      fix_strand=True )
     main( interval, coverage )
     temp_file.close()
-    coverage.close()
\ No newline at end of file
+    coverage.close()

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
--- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
+++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
@@ -26,4 +26,4 @@
     FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -14,7 +14,7 @@
 from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import get_headers, get_test_fname
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 import dataproviders
 
 log = logging.getLogger(__name__)
@@ -272,7 +272,7 @@
         while cursor and ck_data[-1] != '\n':
             ck_data += cursor
             cursor = f.read(1)
-        return to_json_string( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } )
+        return dumps( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } )
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
         preview = util.string_as_bool( preview )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/datatypes/util/__init__.py
--- a/lib/galaxy/datatypes/util/__init__.py
+++ b/lib/galaxy/datatypes/util/__init__.py
@@ -1,3 +1,3 @@
 """
 Utilities for Galaxy datatypes.
-"""
\ No newline at end of file
+"""

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/external_services/result_handlers/basic.py
--- a/lib/galaxy/external_services/result_handlers/basic.py
+++ b/lib/galaxy/external_services/result_handlers/basic.py
@@ -1,4 +1,4 @@
-from galaxy.util.json import to_json_string, from_json_string
+from galaxy.util.json import dumps, loads
 from galaxy.util.template import fill_template
 import logging
 
@@ -44,7 +44,7 @@
     type = 'json_display'
 
     def handle_result( self, result, param_dict, trans ):
-        rval = from_json_string( result.content )
+        rval = loads( result.content )
         return trans.fill_template( '/external_services/generic_json.mako', result = rval, param_dict = param_dict, action=self.parent )
 
 class ExternalServiceActionJQueryGridResultHandler( ExternalServiceActionResultHandler ):
@@ -53,7 +53,7 @@
     type = 'jquery_grid'
 
     def handle_result( self, result, param_dict, trans ):
-        rval = from_json_string( result.content )
+        rval = loads( result.content )
         return trans.fill_template( '/external_services/generic_jquery_grid.mako', result = rval, param_dict = param_dict, action=self.parent )
 
 result_type_to_class = {}

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -25,7 +25,7 @@
 from galaxy.jobs.runners import BaseJobRunner, JobState
 from galaxy.util.bunch import Bunch
 from galaxy.util.expressions import ExpressionContext
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 from galaxy.util import unicodify
 
 from .output_checker import check_output
@@ -723,7 +723,7 @@
         self.job_runner_mapper = JobRunnerMapper( self, queue.dispatcher.url_to_destination, self.app.job_config )
         self.params = None
         if job.params:
-            self.params = from_json_string( job.params )
+            self.params = loads( job.params )
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination( from_job=job )
 
@@ -1390,7 +1390,7 @@
         if os.path.exists( meta_file ):
             for line in open( meta_file, 'r' ):
                 try:
-                    line = from_json_string( line )
+                    line = loads( line )
                     assert 'type' in line
                 except:
                     log.exception( '(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % self.job_id )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/jobs/actions/__init__.py
--- a/lib/galaxy/jobs/actions/__init__.py
+++ b/lib/galaxy/jobs/actions/__init__.py
@@ -1,4 +1,4 @@
 """
 This package contains job action classes.
 
-"""
\ No newline at end of file
+"""

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/jobs/actions/post.py
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -5,7 +5,7 @@
 import datetime
 import logging
 from galaxy.util import send_mail
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 
 log = logging.getLogger( __name__ )
 
@@ -461,7 +461,7 @@
             else:
                 # Not pja stuff.
                 pass
-        return to_json_string(npd)
+        return dumps(npd)
 
     @classmethod
     def get_add_list(cls):

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
--- a/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
+++ b/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
@@ -83,7 +83,7 @@
                 return self.job_states.INVALID
             url = 'http://' + job.params[ 'smrt_host' ] + self.api_path + '/Jobs/' + job.params[ 'smrt_job_id' ] + '/Status'
             r = urllib2.urlopen( url )
-            status = json.from_json_string( r.read() )
+            status = json.loads( r.read() )
             # TODO: error handling: unexpected json or bad response, bad url, etc.
             if status[ 'Code' ] == 'Completed':
                 log.debug( "SMRT Portal job '%s' is Completed.  Initiating transfer." % job.params[ 'smrt_job_id' ] )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/jobs/transfer_manager.py
--- a/lib/galaxy/jobs/transfer_manager.py
+++ b/lib/galaxy/jobs/transfer_manager.py
@@ -82,7 +82,7 @@
                     sock = socket.socket( socket.AF_INET, socket.SOCK_STREAM )
                     sock.settimeout( 5 )
                     sock.connect( ( 'localhost', tj.socket ) )
-                    sock.send( json.to_json_string( request ) )
+                    sock.send( json.dumps( request ) )
                     response = sock.recv( 8192 )
                     valid, response = json.validate_jsonrpc_response( response, id=request['id'] )
                     if not valid:

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/managers/base.py
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -1,7 +1,120 @@
+from galaxy import exceptions
+
+from galaxy import model
+from galaxy.model import tool_shed_install
+
+
+import logging
+log = logging.getLogger( __name__ )
 
 
 class ModelManager( object ):
     pass
 
+
 class ModelSerializer( object ):
     pass
+
+
+def security_check( trans, item, check_ownership=False, check_accessible=False ):
+    """ Security checks for an item: checks if (a) user owns item or (b) item
+    is accessible to user. This is a generic method for dealing with objects
+    uniformly from the older controller mixin code - however whenever possible
+    the managers for a particular model should be used to perform security
+    checks.
+    """
+
+    # all items are accessible to an admin
+    if trans.user_is_admin():
+        return item
+
+    # Verify ownership: there is a current user and that user is the same as the item's
+    if check_ownership:
+        if not trans.user:
+            raise exceptions.ItemOwnershipException( "Must be logged in to manage Galaxy items", type='error' )
+        if item.user != trans.user:
+            raise exceptions.ItemOwnershipException( "%s is not owned by the current user" % item.__class__.__name__, type='error' )
+
+    # Verify accessible:
+    #   if it's part of a lib - can they access via security
+    #   if it's something else (sharable) have they been added to the item's users_shared_with_dot_users
+    if check_accessible:
+        if type( item ) in ( trans.app.model.LibraryFolder, trans.app.model.LibraryDatasetDatasetAssociation, trans.app.model.LibraryDataset ):
+            if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), item, trans.user ):
+                raise exceptions.ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' )
+        else:
+            if ( item.user != trans.user ) and ( not item.importable ) and ( trans.user not in item.users_shared_with_dot_users ):
+                raise exceptions.ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' )
+    return item
+
+
+def get_class( class_name ):
+    """ Returns the class object that a string denotes. Without this method, we'd have to do eval(<class_name>). """
+    if class_name == 'History':
+        item_class = model.History
+    elif class_name == 'HistoryDatasetAssociation':
+        item_class = model.HistoryDatasetAssociation
+    elif class_name == 'Page':
+        item_class = model.Page
+    elif class_name == 'StoredWorkflow':
+        item_class = model.StoredWorkflow
+    elif class_name == 'Visualization':
+        item_class = model.Visualization
+    elif class_name == 'Tool':
+        item_class = model.Tool
+    elif class_name == 'Job':
+        item_class = model.Job
+    elif class_name == 'User':
+        item_class = model.User
+    elif class_name == 'Group':
+        item_class = model.Group
+    elif class_name == 'Role':
+        item_class = model.Role
+    elif class_name == 'Quota':
+        item_class = model.Quota
+    elif class_name == 'Library':
+        item_class = model.Library
+    elif class_name == 'LibraryFolder':
+        item_class = model.LibraryFolder
+    elif class_name == 'LibraryDatasetDatasetAssociation':
+        item_class = model.LibraryDatasetDatasetAssociation
+    elif class_name == 'LibraryDataset':
+        item_class = model.LibraryDataset
+    elif class_name == 'ToolShedRepository':
+        item_class = tool_shed_install.ToolShedRepository
+    else:
+        item_class = None
+    return item_class
+
+
+def get_object( trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None ):
+    """
+    Convenience method to get a model object with the specified checks. This is
+    a generic method for dealing with objects uniformly from the older
+    controller mixin code - however whenever possible the managers for a
+    particular model should be used to load objects.
+    """
+    try:
+        decoded_id = trans.security.decode_id( id )
+    except:
+        raise exceptions.MessageException( "Malformed %s id ( %s ) specified, unable to decode"
+                                           % ( class_name, str( id ) ), type='error' )
+    try:
+        item_class = get_class( class_name )
+        assert item_class is not None
+        item = trans.sa_session.query( item_class ).get( decoded_id )
+        assert item is not None
+    except Exception:
+        log.exception( "Invalid %s id ( %s ) specified." % ( class_name, id ) )
+        raise exceptions.MessageException( "Invalid %s id ( %s ) specified" % ( class_name, id ), type="error" )
+
+    if check_ownership or check_accessible:
+        security_check( trans, item, check_ownership, check_accessible )
+    if deleted is True and not item.deleted:
+        raise exceptions.ItemDeletionException( '%s "%s" is not deleted'
+                                                % ( class_name, getattr( item, 'name', id ) ), type="warning" )
+    elif deleted is False and item.deleted:
+        raise exceptions.ItemDeletionException( '%s "%s" is deleted'
+                                                % ( class_name, getattr( item, 'name', id ) ), type="warning" )
+    return item
+

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/managers/collections.py
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -1,1 +1,291 @@
-""" Future home of dataset collections managers. """
+from galaxy.dataset_collections.registry import DatasetCollectionTypesRegistry
+from galaxy.dataset_collections.matching import MatchingCollections
+from galaxy.dataset_collections.type_description import CollectionTypeDescriptionFactory
+
+from galaxy import model
+from galaxy.exceptions import MessageException
+from galaxy.exceptions import ItemAccessibilityException
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.managers import hdas  # TODO: Refactor all mixin use into managers.
+from galaxy.managers import histories
+from galaxy.managers import lddas
+from galaxy.managers import tags
+from galaxy.managers.collections_util import validate_input_element_identifiers
+from galaxy.util import validation
+from galaxy.util import odict
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+ERROR_INVALID_ELEMENTS_SPECIFICATION = "Create called with invalid parameters, must specify element identifiers."
+ERROR_NO_COLLECTION_TYPE = "Create called without specifing a collection type."
+
+
+class DatasetCollectionManager( object ):
+    """
+    Abstraction for interfacing with dataset collections instance - ideally abstarcts
+    out model and plugin details.
+    """
+
+    def __init__( self, app ):
+        self.type_registry = DatasetCollectionTypesRegistry( app )
+        self.collection_type_descriptions = CollectionTypeDescriptionFactory( self.type_registry )
+        self.model = app.model
+        self.security = app.security
+        self.hda_manager = hdas.HDAManager()
+        self.history_manager = histories.HistoryManager()
+        self.tag_manager = tags.TagsManager( app )
+        self.ldda_manager = lddas.LDDAManager( )
+
+    def create(
+        self,
+        trans,
+        parent,  # PRECONDITION: security checks on ability to add to parent occurred during load.
+        name,
+        collection_type,
+        element_identifiers=None,
+        elements=None,
+        implicit_collection_info=None,
+    ):
+        """
+        """
+        # Trust embedded, newly created objects created by tool subsystem.
+        trusted_identifiers = implicit_collection_info is not None
+
+        if element_identifiers and not trusted_identifiers:
+            validate_input_element_identifiers( element_identifiers )
+
+        dataset_collection = self.__create_dataset_collection(
+            trans=trans,
+            collection_type=collection_type,
+            element_identifiers=element_identifiers,
+            elements=elements,
+        )
+        if isinstance( parent, model.History ):
+            dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
+                collection=dataset_collection,
+                name=name,
+            )
+            if implicit_collection_info:
+                for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]:
+                    dataset_collection_instance.add_implicit_input_collection( input_name, input_collection )
+                for output_dataset in implicit_collection_info.get( "outputs" ):
+                    output_dataset.hidden_beneath_collection_instance = dataset_collection_instance
+                    trans.sa_session.add( output_dataset )
+
+                dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ]
+            log.debug("Created collection with %d elements" % ( len( dataset_collection_instance.collection.elements ) ) )
+            # Handle setting hid
+            parent.add_dataset_collection( dataset_collection_instance )
+        elif isinstance( parent, model.LibraryFolder ):
+            dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation(
+                collection=dataset_collection,
+                folder=parent,
+                name=name,
+            )
+        else:
+            message = "Internal logic error - create called with unknown parent type %s" % type( parent )
+            log.exception( message )
+            raise MessageException( message )
+
+        return self.__persist( dataset_collection_instance )
+
+    def __create_dataset_collection(
+        self,
+        trans,
+        collection_type,
+        element_identifiers=None,
+        elements=None,
+    ):
+        if element_identifiers is None and elements is None:
+            raise RequestParameterInvalidException( ERROR_INVALID_ELEMENTS_SPECIFICATION )
+        if not collection_type:
+            raise RequestParameterInvalidException( ERROR_NO_COLLECTION_TYPE )
+        collection_type_description = self.collection_type_descriptions.for_collection_type( collection_type )
+        # If we have elements, this is an internal request, don't need to load
+        # objects from identifiers.
+        if elements is None:
+            if collection_type_description.has_subcollections( ):
+                # Nested collection - recursively create collections and update identifiers.
+                self.__recursively_create_collections( trans, element_identifiers )
+            elements = self.__load_elements( trans, element_identifiers )
+        # else if elements is set, it better be an ordered dict!
+
+        type_plugin = collection_type_description.rank_type_plugin()
+        dataset_collection = type_plugin.build_collection( elements )
+        dataset_collection.collection_type = collection_type
+        return dataset_collection
+
+    def delete( self, trans, instance_type, id ):
+        dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True )
+        dataset_collection_instance.deleted = True
+        trans.sa_session.add( dataset_collection_instance )
+        trans.sa_session.flush( )
+
+    def update( self, trans, instance_type, id, payload ):
+        dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True )
+        if trans.user is None:
+            anon_allowed_payload = {}
+            if 'deleted' in payload:
+                anon_allowed_payload[ 'deleted' ] = payload[ 'deleted' ]
+            if 'visible' in payload:
+                anon_allowed_payload[ 'visible' ] = payload[ 'visible' ]
+            payload = self._validate_and_parse_update_payload( anon_allowed_payload )
+        else:
+            payload = self._validate_and_parse_update_payload( payload )
+        changed = self._set_from_dict( trans, dataset_collection_instance, payload )
+        return changed
+
+    def copy(
+        self,
+        trans,
+        parent,  # PRECONDITION: security checks on ability to add to parent occurred during load.
+        source,
+        encoded_source_id,
+    ):
+        assert source == "hdca"  # for now
+        source_hdca = self.__get_history_collection_instance( trans, encoded_source_id )
+        new_hdca = source_hdca.copy()
+        parent.add_dataset_collection( new_hdca )
+        trans.sa_session.add( new_hdca )
+        trans.sa_session.flush()
+        return source_hdca
+
+    def _set_from_dict( self, trans, dataset_collection_instance, new_data ):
+        # Blatantly stolen from UsesHistoryDatasetAssociationMixin.set_hda_from_dict.
+
+        # send what we can down into the model
+        changed = dataset_collection_instance.set_from_dict( new_data )
+        # the rest (often involving the trans) - do here
+        if 'annotation' in new_data.keys() and trans.get_user():
+            dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] )
+            changed[ 'annotation' ] = new_data[ 'annotation' ]
+        if 'tags' in new_data.keys() and trans.get_user():
+            self.tag_manager.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user )
+
+        if changed.keys():
+            trans.sa_session.flush()
+
+        return changed
+
+    def _validate_and_parse_update_payload( self, payload ):
+        validated_payload = {}
+        for key, val in payload.items():
+            if val is None:
+                continue
+            if key in ( 'name' ):
+                val = validation.validate_and_sanitize_basestring( key, val )
+                validated_payload[ key ] = val
+            if key in ( 'deleted', 'visible' ):
+                validated_payload[ key ] = validation.validate_boolean( key, val )
+            elif key == 'tags':
+                validated_payload[ key ] = validation.validate_and_sanitize_basestring_list( key, val )
+        return validated_payload
+
+    def history_dataset_collections(self, history, query):
+        collections = history.active_dataset_collections
+        collections = filter( query.direct_match, collections )
+        return collections
+
+    def __persist( self, dataset_collection_instance ):
+        context = self.model.context
+        context.add( dataset_collection_instance )
+        context.flush()
+        return dataset_collection_instance
+
+    def __recursively_create_collections( self, trans, element_identifiers ):
+        for index, element_identifier in enumerate( element_identifiers ):
+            try:
+                if not element_identifier[ "src" ] == "new_collection":
+                    # not a new collection, keep moving...
+                    continue
+            except KeyError:
+                # Not a dictionary, just an id of an HDA - move along.
+                continue
+
+            # element identifier is a dict with src new_collection...
+            collection_type = element_identifier.get( "collection_type", None )
+            collection = self.__create_dataset_collection(
+                trans=trans,
+                collection_type=collection_type,
+                element_identifiers=element_identifier[ "element_identifiers" ],
+            )
+            element_identifier[ "__object__" ] = collection
+
+        return element_identifiers
+
+    def __load_elements( self, trans, element_identifiers ):
+        elements = odict.odict()
+        for element_identifier in element_identifiers:
+            elements[ element_identifier[ "name" ] ] = self.__load_element( trans, element_identifier )
+        return elements
+
+    def __load_element( self, trans, element_identifier ):
+        #if not isinstance( element_identifier, dict ):
+        #    # Is allowing this to just be the id of an hda too clever? Somewhat
+        #    # consistent with other API methods though.
+        #    element_identifier = dict( src='hda', id=str( element_identifier ) )
+
+        # Previously created collection already found in request, just pass
+        # through as is.
+        if "__object__" in element_identifier:
+            return element_identifier[ "__object__" ]
+
+        # dateset_identifier is dict {src=hda|ldda|hdca|new_collection, id=<encoded_id>}
+        try:
+            src_type = element_identifier.get( 'src', 'hda' )
+        except AttributeError:
+            raise MessageException( "Dataset collection element definition (%s) not dictionary-like." % element_identifier )
+        encoded_id = element_identifier.get( 'id', None )
+        if not src_type or not encoded_id:
+            raise RequestParameterInvalidException( "Problem decoding element identifier %s" % element_identifier )
+
+        if src_type == 'hda':
+            decoded_id = int( trans.app.security.decode_id( encoded_id ) )
+            element = self.hda_manager.get( trans, decoded_id, check_ownership=False )
+        elif src_type == 'ldda':
+            element = self.ldda_manager.get( trans, encoded_id )
+        elif src_type == 'hdca':
+            # TODO: Option to copy? Force copy? Copy or allow if not owned?
+            element = self.__get_history_collection_instance( trans, encoded_id ).collection
+        # TODO: ldca.
+        else:
+            raise RequestParameterInvalidException( "Unknown src_type parameter supplied '%s'." % src_type )
+        return element
+
+    def match_collections( self, collections_to_match ):
+        """
+        May seem odd to place it here, but planning to grow sophistication and
+        get plugin types involved so it will likely make sense in the future.
+        """
+        return MatchingCollections.for_collections( collections_to_match, self.collection_type_descriptions )
+
+    def get_dataset_collection_instance( self, trans, instance_type, id, **kwds ):
+        """
+        """
+        if instance_type == "history":
+            return self.__get_history_collection_instance( trans, id, **kwds )
+        elif instance_type == "library":
+            return self.__get_library_collection_instance( trans, id, **kwds )
+
+    def get_dataset_collection( self, trans, encoded_id ):
+        collection_id = int( trans.app.security.decode_id( encoded_id ) )
+        collection = trans.sa_session.query( trans.app.model.DatasetCollection ).get( collection_id )
+        return collection
+
+    def __get_history_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ):
+        instance_id = int( trans.app.security.decode_id( id ) )
+        collection_instance = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( instance_id )
+        self.history_manager.secure( trans, collection_instance.history, check_ownership=check_ownership, check_accessible=check_accessible )
+        return collection_instance
+
+    def __get_library_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ):
+        if check_ownership:
+            raise NotImplemented( "Functionality (getting library dataset collection with ownership check) unimplemented." )
+        instance_id = int( trans.security.decode_id( id ) )
+        collection_instance = trans.sa_session.query( trans.app.model.LibraryDatasetCollectionAssociation ).get( instance_id )
+        if check_accessible:
+            if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), collection_instance, trans.user ):
+                raise ItemAccessibilityException( "LibraryDatasetCollectionAssociation is not accessible to the current user", type='error' )
+        return collection_instance

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/managers/context.py
--- a/lib/galaxy/managers/context.py
+++ b/lib/galaxy/managers/context.py
@@ -4,7 +4,7 @@
 
 import os
 
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.util import bunch
 
 class ProvidesAppContext( object ):
@@ -19,7 +19,7 @@
         Application-level logging of user actions.
         """
         if self.app.config.log_actions:
-            action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) )
+            action = self.app.model.UserAction(action=action, context=context, params=unicode( dumps( params ) ) )
             try:
                 if user:
                     action.user = user

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/managers/lddas.py
--- /dev/null
+++ b/lib/galaxy/managers/lddas.py
@@ -0,0 +1,16 @@
+from galaxy.managers import base as manager_base
+
+
+class LDDAManager( manager_base.ModelManager ):
+    """ A fairly sparse manager for LDDAs.
+    """
+
+    def __init__( self ):
+        """
+        Set up and initialize other managers needed by lddas.
+        """
+        pass
+
+    def get( self, trans, id, check_accessible=True ):
+        return manager_base.get_object( trans, id, 'LibraryDatasetDatasetAssociation',
+                                        check_ownership=False, check_accessible=check_accessible )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/managers/tags.py
--- /dev/null
+++ b/lib/galaxy/managers/tags.py
@@ -0,0 +1,20 @@
+
+
+class TagsManager( object ):
+    """ Manages CRUD operations related to tagging objects.
+    """
+
+    def __init__( self, app ):
+        self.app = app
+        self.tag_handler = app.tag_handler
+
+    def set_tags_from_list( self, trans, item, new_tags_list, user=None ):
+        #precondition: item is already security checked against user
+        #precondition: incoming tags is a list of sanitized/formatted strings
+        user = user or trans.user
+
+        self.tag_handler.delete_item_tags( trans, user, item )
+        new_tags_str = ','.join( new_tags_list )
+        self.tag_handler.apply_item_tags( trans, user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) )
+        trans.sa_session.flush()
+        return item.tags

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/item_attrs.py
--- a/lib/galaxy/model/item_attrs.py
+++ b/lib/galaxy/model/item_attrs.py
@@ -4,6 +4,7 @@
 import galaxy
 import logging
 import datetime
+import uuid
 
 log = logging.getLogger( __name__ )
 
@@ -186,6 +187,8 @@
                     return value_mapper.get( key )( item )
                 if type(item) == datetime.datetime:
                     return item.isoformat()
+                elif type(item) == uuid.UUID:
+                    return str(item)
                 # Leaving this for future reference, though we may want a more
                 # generic way to handle special type mappings going forward.
                 # If the item is of a class that needs to be 'stringified' before being put into a JSON data structure

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
--- a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
+++ b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
@@ -10,7 +10,7 @@
 from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow
@@ -62,7 +62,7 @@
     for r in result:
         sample_id = r[0]
         if r[1]:
-            dataset_files = from_json_string(r[1])
+            dataset_files = loads(r[1])
             for df in dataset_files:
                 if type(df) == type(dict()):
                     cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')"

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
--- a/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
+++ b/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
@@ -6,7 +6,7 @@
 from sqlalchemy.orm import *
 from migrate import *
 from migrate.changeset import *
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 
 import logging
 log = logging.getLogger( __name__ )
@@ -41,7 +41,7 @@
         viz_id = viz['viz_id']
         viz_rev_id = viz['viz_rev_id']
         if viz[Visualization_revision_table.c.config]:
-            dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'")
+            dbkey = loads(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'")
             migrate_engine.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id))
             migrate_engine.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id))
 

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0057_request_notify.py
--- a/lib/galaxy/model/migrate/versions/0057_request_notify.py
+++ b/lib/galaxy/model/migrate/versions/0057_request_notify.py
@@ -10,7 +10,7 @@
 from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow
@@ -46,13 +46,13 @@
             id = int(r[0])
             notify_old = r[1]
             notify_new = dict(email=[], sample_states=[], body='', subject='')
-            cmd = "update request set notification='%s' where id=%i" % (to_json_string(notify_new), id)
+            cmd = "update request set notification='%s' where id=%i" % (dumps(notify_new), id)
             migrate_engine.execute( cmd )
 
         cmd = "SELECT id, notification FROM request"
         result = migrate_engine.execute( cmd )
         for r in result:
-            rr = from_json_string(str(r[1]))
+            rr = loads(str(r[1]))
 
         # remove the 'notify' column for non-sqlite databases.
         if migrate_engine.name != 'sqlite':

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
--- a/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
+++ b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
@@ -10,7 +10,7 @@
 from sqlalchemy.exc import *
 
 from galaxy.model.custom_types import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
--- a/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
+++ b/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
@@ -9,7 +9,7 @@
 from migrate import *
 from migrate.changeset import *
 from sqlalchemy.exc import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 from galaxy.model.custom_types import _sniffnfix_pg9_hex
 
 import datetime
@@ -53,13 +53,13 @@
         fields = str( row[1] )
         if not fields.strip():
             continue
-        fields_list = from_json_string( _sniffnfix_pg9_hex( fields ) )
+        fields_list = loads( _sniffnfix_pg9_hex( fields ) )
         if len( fields_list ):
             for index, field in enumerate( fields_list ):
                 field[ 'name' ] = 'field_%i' % index
                 field[ 'helptext' ] = field[ 'helptext' ].replace("'", "''").replace('"', "")
                 field[ 'label' ] = field[ 'label' ].replace("'", "''")
-            fields_json = to_json_string( fields_list )
+            fields_json = dumps( fields_list )
             if migrate_engine.name == 'mysql':
                 cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( fields_json, form_definition_id )
             else:
@@ -76,16 +76,16 @@
         if not str( row[1] ).strip():
             continue
         row1 = str(row[1]).replace('\n', '').replace('\r', '')
-        values_list = from_json_string( str( row1 ).strip() )
+        values_list = loads( str( row1 ).strip() )
         if not str( row[2] ).strip():
             continue
-        fields_list = from_json_string( str( row[2] ).strip() )
+        fields_list = loads( str( row[2] ).strip() )
         if fields_list and type(values_list) == type(list()):
             values_dict = {}
             for field_index, field in enumerate( fields_list ):
                 field_name = field[ 'name' ]
                 values_dict[ field_name ] = get_value(values_list, field_index )
-            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( to_json_string( values_dict ), form_values_id )
+            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( dumps( values_dict ), form_values_id )
             migrate_engine.execute( cmd )
 
 def downgrade(migrate_engine):
@@ -110,17 +110,17 @@
         form_values_id = int( row[0] )
         if not str( row[1] ).strip():
             continue
-        values_dict = from_json_string( str( row[1] ) )
+        values_dict = loads( str( row[1] ) )
         if not str( row[2] ).strip():
             continue
-        fields_list = from_json_string( str( row[2] ) )
+        fields_list = loads( str( row[2] ) )
         if fields_list:
             values_list = []
             for field_index, field in enumerate( fields_list ):
                 field_name = field[ 'name' ]
                 field_value = values_dict[ field_name ]
                 values_list.append( field_value )
-            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( to_json_string( values_list ), form_values_id )
+            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( dumps( values_list ), form_values_id )
             migrate_engine.execute( cmd )
     # remove name attribute from the field column of the form_definition table
     cmd = "SELECT f.id, f.fields FROM form_definition AS f"
@@ -130,13 +130,13 @@
         fields = str( row[1] )
         if not fields.strip():
             continue
-        fields_list = from_json_string( _sniffnfix_pg9_hex( fields ) )
+        fields_list = loads( _sniffnfix_pg9_hex( fields ) )
         if len( fields_list ):
             for index, field in enumerate( fields_list ):
                 if field.has_key( 'name' ):
                     del field[ 'name' ]
             if migrate_engine.name == 'mysql':
-                cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( to_json_string( fields_list ), form_definition_id )
+                cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( dumps( fields_list ), form_definition_id )
             else:
-                cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( to_json_string( fields_list ), form_definition_id )
+                cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( dumps( fields_list ), form_definition_id )
         migrate_engine.execute( cmd )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
--- a/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
+++ b/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
@@ -13,7 +13,7 @@
 
 from galaxy.model.custom_types import *
 
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow
@@ -104,7 +104,7 @@
                                      'layout': 'none',
                                      'default': '' } )
     form_definition_type = 'Sequencer Information Form'
-    form_definition_layout = to_json_string('[]')
+    form_definition_layout = dumps('[]')
     cmd = "INSERT INTO form_definition VALUES ( %s, %s, %s, '%s', '%s', %s, '%s', '%s', '%s' )"
     cmd = cmd % ( nextval( 'form_definition' ),
                   localtimestamp(),
@@ -112,7 +112,7 @@
                   form_definition_name,
                   form_definition_desc,
                   form_definition_current_id,
-                  to_json_string( form_definition_fields ),
+                  dumps( form_definition_fields ),
                   form_definition_type,
                   form_definition_layout )
     migrate_engine.execute( cmd )
@@ -134,7 +134,7 @@
         values = str( row[1] )
         if not values.strip():
             continue
-        values = from_json_string( values )
+        values = loads( values )
         # proceed only if sequencer_info is a valid list
         if values and type( values ) == type( dict() ):
             if sequencer_info.get( 'host', '' ) == values.get( 'field_0', '' ) \
@@ -148,7 +148,7 @@
 def add_sequencer( sequencer_index, sequencer_form_definition_id, sequencer_info ):
     '''Adds a new sequencer to the sequencer table along with its form values.'''
     # Create a new form values record with the supplied sequencer information
-    values = to_json_string( { 'field_0': sequencer_info.get( 'host', '' ),
+    values = dumps( { 'field_0': sequencer_info.get( 'host', '' ),
                                'field_1': sequencer_info.get( 'username', '' ),
                                'field_2': sequencer_info.get( 'password', '' ),
                                'field_3': sequencer_info.get( 'data_dir', '' ),
@@ -233,7 +233,7 @@
             # skip if sequencer_info is empty
             if not sequencer_info.strip() or sequencer_info in ['None', 'null']:
                 continue
-            sequencer_info = from_json_string( sequencer_info.strip() )
+            sequencer_info = loads( sequencer_info.strip() )
             # proceed only if sequencer_info is a valid dict
             if sequencer_info and type( sequencer_info ) == type( dict() ):
                 # check if this sequencer has already been added to the sequencer table
@@ -277,9 +277,9 @@
         result = migrate_engine.execute( cmd )
         for row in result:
             request_type_id = row[0]
-            seq_values = from_json_string( str( row[1] ) )
+            seq_values = loads( str( row[1] ) )
             # create the datatx_info json dict
-            datatx_info = to_json_string( dict( host = seq_values.get( 'field_0', '' ),
+            datatx_info = dumps( dict( host = seq_values.get( 'field_0', '' ),
                                                 username = seq_values.get( 'field_1', '' ),
                                                 password = seq_values.get( 'field_2', '' ),
                                                 data_dir = seq_values.get( 'field_3', '' ),

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
--- a/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
+++ b/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
@@ -15,7 +15,7 @@
 
 from galaxy.model.custom_types import *
 
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import datetime
 now = datetime.datetime.utcnow

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
--- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
+++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
@@ -9,7 +9,7 @@
 from sqlalchemy.exc import *
 import binascii
 
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import logging
 log = logging.getLogger( __name__ )
@@ -42,11 +42,11 @@
         # first check if loading the dict from the json succeeds
         # if that fails, it means that the content field is corrupted.
         try:
-            field_values_dict = from_json_string( _sniffnfix_pg9_hex( str( row['field_values'] ) ) )
+            field_values_dict = loads( _sniffnfix_pg9_hex( str( row['field_values'] ) ) )
         except Exception, e:
             corrupted_rows = corrupted_rows + 1
             # content field is corrupted
-            fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) )
+            fields_list = loads( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) )
             field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) )
             try:
                 #Encoding errors?  Just to be safe.
@@ -85,7 +85,7 @@
                     # add to the new values dict
                     field_values_dict[ field['name'] ] = value
             # update the db
-            json_values = to_json_string(field_values_dict)
+            json_values = dumps(field_values_dict)
             cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) )
             migrate_engine.execute( cmd )
             try:

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
--- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
+++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
@@ -12,7 +12,7 @@
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import *
 from galaxy.model.custom_types import _sniffnfix_pg9_hex
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 
 import sys, logging
 log = logging.getLogger( __name__ )
@@ -77,7 +77,7 @@
     for row in result:
         if row[1]:
             tool_shed_repository_id = row[0]
-            repository_metadata = from_json_string( _sniffnfix_pg9_hex( str( row[1] ) ) )
+            repository_metadata = loads( _sniffnfix_pg9_hex( str( row[1] ) ) )
             # Create a new row in the tool table for each tool included in repository.  We will NOT
             # handle tool_version_associaions because we do not have the information we need to do so.
             tools = repository_metadata.get( 'tools', [] )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
--- a/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
+++ b/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
@@ -22,4 +22,4 @@
     try:
         user.c.password.alter(type=String(40))
     except:
-        log.exception( "Altering password column failed" )
\ No newline at end of file
+        log.exception( "Altering password column failed" )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/migrate/versions/0117_add_user_activation.py
--- a/lib/galaxy/model/migrate/versions/0117_add_user_activation.py
+++ b/lib/galaxy/model/migrate/versions/0117_add_user_activation.py
@@ -54,4 +54,4 @@
         user_active.drop()
         user_activation_token.drop()
     except Exception, e:
-        log.debug( "Dropping 'active' and 'activation_token' columns from galaxy_user table failed: %s" % ( str( e ) ) )
\ No newline at end of file
+        log.debug( "Dropping 'active' and 'activation_token' columns from galaxy_user table failed: %s" % ( str( e ) ) )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/orm/logging_connection_proxy.py
--- a/lib/galaxy/model/orm/logging_connection_proxy.py
+++ b/lib/galaxy/model/orm/logging_connection_proxy.py
@@ -45,4 +45,4 @@
         self.trace_logger.log( "sqlalchemy_query",
             message="Query executed", statement=statement, parameters=parameters,
             executemany=executemany, duration=duration )
-        return rval
\ No newline at end of file
+        return rval

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/model/search.py
--- a/lib/galaxy/model/search.py
+++ b/lib/galaxy/model/search.py
@@ -39,7 +39,7 @@
 Page, PageRevision)
 from galaxy.model.tool_shed_install import ToolVersion
 
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from sqlalchemy import and_
 from sqlalchemy.orm import aliased
 
@@ -429,7 +429,7 @@
         and_(
             Job.id == alias.job_id,
             alias.name == param_name,
-            alias.value == to_json_string(right)
+            alias.value == dumps(right)
         )
     )
 

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/openid/__init__.py
--- a/lib/galaxy/openid/__init__.py
+++ b/lib/galaxy/openid/__init__.py
@@ -1,3 +1,3 @@
 """
 OpenID functionality
-"""
\ No newline at end of file
+"""

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -756,7 +756,6 @@
                         tarball_files.append( ( filesystem_path, tarball_path ) )
                         image_found = True
                         tool_xml = tool_xml.replace( '${static_path}/%s' % tarball_path, tarball_path )
-                    log.debug( tarball_files )
             # If one or more tool help images were found, add the modified tool XML to the tarball instead of the original.
             if image_found:
                 fd, new_tool_config = tempfile.mkstemp( suffix='.xml' )
@@ -817,8 +816,7 @@
                             if len( data_table_definitions ) > 0:
                                 # Put the data table definition XML in a temporary file.
                                 table_definition = '<?xml version="1.0" encoding="utf-8"?>\n<tables>\n    %s</tables>'
-                                table_xml = [ data_table.xml_string for data_table in data_table_definitions ]
-                                table_definition = table_definition % '\n'.join( table_xml ) 
+                                table_definition = table_definition % '\n'.join( data_table_definitions ) 
                                 fd, table_conf = tempfile.mkstemp()
                                 os.close( fd )
                                 file( table_conf, 'w' ).write( table_definition )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -4,7 +4,7 @@
 from galaxy.tools.parameters import DataToolParameter
 from galaxy.tools.parameters import DataCollectionToolParameter
 from galaxy.tools.parameters.wrapped import WrappedParameters
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.util.none_like import NoneDataset
 from galaxy.util.odict import odict
 from galaxy.util.template import fill_template
@@ -324,7 +324,7 @@
             job.add_output_dataset( name, dataset )
         job.object_store_id = object_store_populator.object_store_id
         if job_params:
-            job.params = to_json_string( job_params )
+            job.params = dumps( job_params )
         job.set_handler(tool.get_job_handler(job_params))
         trans.sa_session.add( job )
         # Now that we have a job id, we can remap any outputs if this is a rerun and the user chose to continue dependent jobs

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/actions/metadata.py
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -1,7 +1,7 @@
 from __init__ import ToolAction
 from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
 from galaxy.util.odict import odict
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 
 import logging
 log = logging.getLogger( __name__ )
@@ -50,7 +50,7 @@
         if user:
             job.user_id = user.id
         if job_params:
-            job.params = to_json_string( job_params )
+            job.params = dumps( job_params )
         start_job_state = job.state #should be job.states.NEW
         try:
             # For backward compatibility, some tools may not have versions yet.

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/actions/upload_common.py
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -7,7 +7,7 @@
 from galaxy import datatypes, util
 from galaxy.util.odict import odict
 from galaxy.datatypes import sniff
-from galaxy.util.json import to_json_string
+from galaxy.util.json import dumps
 from galaxy.model.orm import eagerload_all
 from galaxy.exceptions import ObjectInvalid
 
@@ -342,7 +342,7 @@
             # user cannot remove it unless the parent directory is writable.
             if link_data_only == 'copy_files' and trans.app.config.external_chown_script:
                 _chown( uploaded_dataset.path )
-        json_file.write( to_json_string( json ) + '\n' )
+        json_file.write( dumps( json ) + '\n' )
     json_file.close()
     if trans.app.config.external_chown_script:
         _chown( json_file_path )
@@ -375,7 +375,7 @@
 
     for name, value in tool.params_to_strings( params, trans.app ).iteritems():
         job.add_parameter( name, value )
-    job.add_parameter( 'paramfile', to_json_string( json_file_path ) )
+    job.add_parameter( 'paramfile', dumps( json_file_path ) )
     object_store_id = None
     for i, dataset in enumerate( data_list ):
         if folder:

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/imp_exp/__init__.py
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -8,7 +8,7 @@
 from galaxy.tools.parameters.basic import UnvalidatedValue
 from galaxy.web.framework.helpers import to_unicode
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.json import loads, dumps
 from galaxy.web.base.controller import UsesHistoryMixin
 
 log = logging.getLogger(__name__)
@@ -108,7 +108,7 @@
                 #
                 history_attr_file_name = os.path.join( archive_dir, 'history_attrs.txt')
                 history_attr_str = read_file_contents( history_attr_file_name )
-                history_attrs = from_json_string( history_attr_str )
+                history_attrs = loads( history_attr_str )
 
                 # Create history.
                 new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), \
@@ -134,12 +134,12 @@
                 #
                 datasets_attrs_file_name = os.path.join( archive_dir, 'datasets_attrs.txt')
                 datasets_attr_str = read_file_contents( datasets_attrs_file_name )
-                datasets_attrs = from_json_string( datasets_attr_str )
-                
+                datasets_attrs = loads( datasets_attr_str )
+
                 if os.path.exists( datasets_attrs_file_name + ".provenance" ):
                     provenance_attr_str = read_file_contents( datasets_attrs_file_name + ".provenance" )
-                    provenance_attrs = from_json_string( provenance_attr_str )
-                    datasets_attrs += provenance_attrs                    
+                    provenance_attrs = loads( provenance_attr_str )
+                    datasets_attrs += provenance_attrs
 
                 # Get counts of how often each dataset file is used; a file can
                 # be linked to multiple dataset objects (HDAs).
@@ -230,7 +230,7 @@
                             return self.sa_session.query( model.HistoryDatasetAssociation ) \
                                             .filter_by( history=new_history, hid=obj_dct['hid'] ).first()
                     return obj_dct
-                jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda )
+                jobs_attrs = loads( jobs_attr_str, object_hook=as_hda )
 
                 # Create each job.
                 for job_attrs in jobs_attrs:
@@ -279,7 +279,7 @@
                                             .filter_by( history=new_history, hid=value.hid ).first()
                             value = input_hda.id
                         #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id )
-                        imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) )
+                        imported_job.add_parameter( name, dumps( value, cls=HistoryDatasetAssociationIDEncoder ) )
 
                     # TODO: Connect jobs to input datasets.
 
@@ -292,14 +292,14 @@
                             imported_job.add_output_dataset( output_hda.name, output_hda )
 
                     # Connect jobs to input datasets.
-                    if 'input_mapping' in job_attrs: 
+                    if 'input_mapping' in job_attrs:
                         for input_name, input_hid in job_attrs[ 'input_mapping' ].items():
                             #print "%s job has input dataset %i" % (imported_job.id, input_hid)
                             input_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \
                                             .filter_by( history=new_history, hid=input_hid ).first()
                             if input_hda:
                                 imported_job.add_input_dataset( input_name, input_hda )
-                            
+
 
                     self.sa_session.flush()
 
@@ -409,7 +409,7 @@
         }
         history_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name
         history_attrs_out = open( history_attrs_filename, 'w' )
-        history_attrs_out.write( to_json_string( history_attrs ) )
+        history_attrs_out.write( dumps( history_attrs ) )
         history_attrs_out.close()
         jeha.history_attrs_filename = history_attrs_filename
 
@@ -427,12 +427,12 @@
                 included_datasets.append( dataset )
         datasets_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name
         datasets_attrs_out = open( datasets_attrs_filename, 'w' )
-        datasets_attrs_out.write( to_json_string( datasets_attrs, cls=HistoryDatasetAssociationEncoder ) )
+        datasets_attrs_out.write( dumps( datasets_attrs, cls=HistoryDatasetAssociationEncoder ) )
         datasets_attrs_out.close()
         jeha.datasets_attrs_filename = datasets_attrs_filename
-        
+
         provenance_attrs_out = open( datasets_attrs_filename + ".provenance", 'w' )
-        provenance_attrs_out.write( to_json_string( provenance_attrs, cls=HistoryDatasetAssociationEncoder ) )
+        provenance_attrs_out.write( dumps( provenance_attrs, cls=HistoryDatasetAssociationEncoder ) )
         provenance_attrs_out.close()
 
         #
@@ -477,7 +477,7 @@
             job_attrs[ 'exit_code' ] = job.exit_code
             job_attrs[ 'create_time' ] = job.create_time.isoformat()
             job_attrs[ 'update_time' ] = job.update_time.isoformat()
-            
+
 
             # Get the job's parameters
             try:
@@ -509,7 +509,7 @@
 
         jobs_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name
         jobs_attrs_out = open( jobs_attrs_filename, 'w' )
-        jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) )
+        jobs_attrs_out.write( dumps( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) )
         jobs_attrs_out.close()
         jeha.jobs_attrs_filename = jobs_attrs_filename
 

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/imp_exp/export_history.py
--- a/lib/galaxy/tools/imp_exp/export_history.py
+++ b/lib/galaxy/tools/imp_exp/export_history.py
@@ -39,7 +39,7 @@
         except OverflowError:
             pass
         datasets_attr_in.close()
-        datasets_attrs = from_json_string( datasets_attr_str )
+        datasets_attrs = loads( datasets_attr_str )
 
         # Add datasets to archive and update dataset attributes.
         # TODO: security check to ensure that files added are in Galaxy dataset directory?
@@ -54,7 +54,7 @@
 
         # Rewrite dataset attributes file.
         datasets_attrs_out = open( datasets_attrs_file, 'w' )
-        datasets_attrs_out.write( to_json_string( datasets_attrs ) )
+        datasets_attrs_out.write( dumps( datasets_attrs ) )
         datasets_attrs_out.close()
 
         # Finish archive.
@@ -80,4 +80,4 @@
 
     # Create archive.
     status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip )
-    print status
\ No newline at end of file
+    print status

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/parameters/__init__.py
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -85,7 +85,7 @@
     for key, value in param_values.iteritems():
         if key in params:
             value = params[ key ].value_to_basic( value, app )
-        rval[ key ] = str( to_json_string( value ) )
+        rval[ key ] = str( dumps( value ) )
     return rval
 
 
@@ -98,7 +98,7 @@
     """
     rval = dict()
     for key, value in param_values.iteritems():
-        value = json_fix( from_json_string( value ) )
+        value = json_fix( loads( value ) )
         if key in params:
             value = params[key].value_from_basic( value, app, ignore_errors )
         rval[ key ] = value

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/tools/util/__init__.py
--- a/lib/galaxy/tools/util/__init__.py
+++ b/lib/galaxy/tools/util/__init__.py
@@ -3,4 +3,4 @@
 
 FIXME: These are used by tool scripts, not the framework, and should not live
        in this package.
-"""
\ No newline at end of file
+"""

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -338,8 +338,8 @@
 
 def pretty_print_json(json_data, is_json_string=False):
     if is_json_string:
-        json_data = json.from_json_string(json_data)
-    return json.to_json_string(json_data, sort_keys=True, indent=4)
+        json_data = json.loads(json_data)
+    return json.dumps(json_data, sort_keys=True, indent=4)
 
 # characters that are valid
 valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/util/backports/__init__.py
--- a/lib/galaxy/util/backports/__init__.py
+++ b/lib/galaxy/util/backports/__init__.py
@@ -1,3 +1,3 @@
 """
 Modules for providing backward compatibility with future versions of Python
-"""
\ No newline at end of file
+"""

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/util/backports/importlib/__init__.py
--- a/lib/galaxy/util/backports/importlib/__init__.py
+++ b/lib/galaxy/util/backports/importlib/__init__.py
@@ -39,4 +39,4 @@
 
     ## Note: this was copied from
     ## http://svn.python.org/projects/python/trunk/Lib/importlib/__init__.py
-    ## on 24 September 2012
\ No newline at end of file
+    ## on 24 September 2012

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/util/dbkeys.py
--- a/lib/galaxy/util/dbkeys.py
+++ b/lib/galaxy/util/dbkeys.py
@@ -3,7 +3,7 @@
 """
 #dbkeys read from disk using builds.txt
 from galaxy.util import read_dbnames
-from galaxy.util.json import from_json_string
+from galaxy.util.json import loads
 import os.path
 
 
@@ -38,7 +38,7 @@
                     rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) )
             user = trans.user
             if user and 'dbkeys' in user.preferences:
-                user_keys = from_json_string( user.preferences['dbkeys'] )
+                user_keys = loads( user.preferences['dbkeys'] )
                 for key, chrom_dict in user_keys.iteritems():
                     rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) )
         # Load old builds.txt static keys
@@ -61,8 +61,8 @@
                 chrom_info = db_dataset.file_name
             else:
                 # Do Custom Build handling
-                if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
-                    custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ]
+                if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in loads( trans.user.preferences[ 'dbkeys' ] ) ):
+                    custom_build_dict = loads( trans.user.preferences[ 'dbkeys' ] )[ dbkey ]
                     # HACK: the attempt to get chrom_info below will trigger the
                     # fasta-to-len converter if the dataset is not available or,
                     # which will in turn create a recursive loop when

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/util/json.py
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -1,14 +1,16 @@
 from __future__ import absolute_import
 
-__all__ = [ "to_json_string", "from_json_string", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
+__all__ = [ "dumps", "loads", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
 
 import json
 import logging
 import random
 import string
 
-to_json_string = json.dumps
-from_json_string = json.loads
+to_json_string = json.dumps  # deprecated
+from_json_string = json.loads  # deprecated
+dumps = json.dumps
+loads = json.loads
 
 log = logging.getLogger( __name__ )
 
@@ -23,12 +25,12 @@
     else:
         return val
 
+
 # Methods for handling JSON-RPC
 
-
 def validate_jsonrpc_request( request, regular_methods, notification_methods ):
     try:
-        request = from_json_string( request )
+        request = loads( request )
     except Exception, e:
         return False, request, jsonrpc_response( id=None,
                                                  error=dict( code=-32700,
@@ -65,7 +67,7 @@
 
 def validate_jsonrpc_response( response, id=None ):
     try:
-        response = from_json_string( response )
+        response = loads( response )
     except Exception, e:
         log.error( 'Response was not valid JSON: %s' % str( e ) )
         log.debug( 'Response was: %s' % response )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/util/log/__init__.py
--- a/lib/galaxy/util/log/__init__.py
+++ b/lib/galaxy/util/log/__init__.py
@@ -2,4 +2,4 @@
 	def __init__( self, name ):
 		self.name = name
 	def log( **kwargs ):
-		raise TypeError( "Abstract Method" )
\ No newline at end of file
+		raise TypeError( "Abstract Method" )

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/util/pastescript/serve.py
--- a/lib/galaxy/util/pastescript/serve.py
+++ b/lib/galaxy/util/pastescript/serve.py
@@ -1056,4 +1056,4 @@
     except BadCommand, e:
         print e.message
         exit_code = e.exit_code
-    sys.exit(exit_code)
\ No newline at end of file
+    sys.exit(exit_code)

diff -r 858c12951cfa764fb8b948e360b29f8a9e90b89b -r d277478dce504dac182886b89192459bc6f83db3 lib/galaxy/visualization/data_providers/__init__.py
--- a/lib/galaxy/visualization/data_providers/__init__.py
+++ b/lib/galaxy/visualization/data_providers/__init__.py
@@ -1,3 +1,3 @@
 """
 Galaxy visualization/visual analysis data providers.
-"""
\ No newline at end of file
+"""

This diff is so big that we needed to truncate the remainder.

https://bitbucket.org/galaxy/galaxy-central/commits/3497f7509b00/
Changeset:   3497f7509b00
User:        martenson
Date:        2014-09-16 15:56:13+00:00
Summary:     trying to merge
Affected #:  35 files

diff -r 80d68ea889c01357b520ecefc56f86b0a44549fc -r 3497f7509b007b04a4db905daf3509f1f3c76626 client/galaxy/scripts/galaxy.library.js
--- a/client/galaxy/scripts/galaxy.library.js
+++ b/client/galaxy/scripts/galaxy.library.js
@@ -47,7 +47,8 @@
     "folders/:folder_id/datasets/:dataset_id"                       : "dataset_detail",
     "folders/:folder_id/datasets/:dataset_id/permissions"           : "dataset_permissions",
     "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id"     : "dataset_version",
-    "folders/:folder_id/download/:format"                           : "download"
+    "folders/:folder_id/download/:format"                           : "download",
+    "folders/:folder_id/import/:source"                             : "import_datasets"
   },
 
   back: function() {
@@ -147,6 +148,15 @@
           }
           Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
        });
+       this.library_router.on('route:import_datasets', function(folder_id, source){
+          if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){
+            Galaxy.libraries.folderToolbarView.showImportModal({source:source});
+          } else {
+            Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id});
+            Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id});
+            Galaxy.libraries.folderToolbarView.showImportModal({source: source});
+          }
+       });
 
     Backbone.history.start({pushState: false});
     }

This diff is so big that we needed to truncate the remainder.

https://bitbucket.org/galaxy/galaxy-central/commits/aec146e3828b/
Changeset:   aec146e3828b
User:        martenson
Date:        2014-09-16 17:15:32+00:00
Summary:     removed bug with missing return
Affected #:  5 files

diff -r 3497f7509b007b04a4db905daf3509f1f3c76626 -r aec146e3828b16812ca24c5f8651ba3d0d483a6a client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -592,13 +592,15 @@
     // need to check which paths to call
     var that = this;
     var popped_item = paths.pop();
-    if (typeof popped_item === "undefined") {
+    if (typeof popped_item == "undefined") {
       if (this.options.chain_call_control.failed_number === 0){
         mod_toastr.success('Selected folders and their contents imported into the current folder');
         Galaxy.modal.hide();
       } else {
+        // TODO better error report
         mod_toastr.error('Something went wrong :(');
       }
+      return true;
     }
     var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
                                                       '&source=' + source +

diff -r 3497f7509b007b04a4db905daf3509f1f3c76626 -r aec146e3828b16812ca24c5f8651ba3d0d483a6a static/scripts/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -592,13 +592,14 @@
     // need to check which paths to call
     var that = this;
     var popped_item = paths.pop();
-    if (typeof popped_item === "undefined") {
+    if (typeof popped_item == "undefined") {
       if (this.options.chain_call_control.failed_number === 0){
         mod_toastr.success('Selected folders and their contents imported into the current folder');
         Galaxy.modal.hide();
       } else {
         mod_toastr.error('Something went wrong :(');
       }
+      return true;
     }
     var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
                                                       '&source=' + source +

diff -r 3497f7509b007b04a4db905daf3509f1f3c76626 -r aec146e3828b16812ca24c5f8651ba3d0d483a6a static/scripts/packed/mvc/library/library-folderrow-view.js
--- a/static/scripts/packed/mvc/library/library-folderrow-view.js
+++ b/static/scripts/packed/mvc/library/library-folderrow-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){h.showDatasetDetails()}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">');tmpl_array.push("  <td>");tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push("  </td>");tmpl_array.push("  <td></td>");tmpl_array.push("  <td>");tmpl_array.push('    <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push("  </td>");tmpl_array.push("  <td>folder</td>");tmpl_array.push("  <td></td>");tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push("  <td>");tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push("  </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">');tmpl_array.push("  <td>");tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push("  </td>");tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push('  <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push("  <td>");tmpl_array.push('    <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push('    <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push('    <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push("  </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push("  <td>");tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push("  </td>");tmpl_array.push("  <td></td>");tmpl_array.push('  <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.model=g;this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var n=h.model.get("folder_id");window.location="#folders/"+n+"/datasets/"+h.id}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">');tmpl_array.push("  <td>");tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push("  </td>");tmpl_array.push("  <td></td>");tmpl_array.push("  <td>");tmpl_array.push('    <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push("  </td>");tmpl_array.push("  <td>folder</td>");tmpl_array.push("  <td></td>");tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push("  <td>");tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push("  </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">');tmpl_array.push("  <td>");tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push("  </td>");tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push('  <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push("  <td>");tmpl_array.push('    <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push('    <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push('    <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push("  </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset library-row" id="<%- content_item.id %>">');tmpl_array.push("  <td>");tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push("  </td>");tmpl_array.push("  <td></td>");tmpl_array.push('  <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}});
\ No newline at end of file

diff -r 3497f7509b007b04a4db905daf3509f1f3c76626 -r aec146e3828b16812ca24c5f8651ba3d0d483a6a static/scripts/packed/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","libs/jquery/jstree","mvc/library/library-model"],function(c,e,f,b,d){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}else{f.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var g=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new d.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";g.push(m)}this.options.chain_call_control.total_number=g.length;jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCall(g,n)},chainCall:function(h,k){var g=this;var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCall(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCall(h,k)})},initProgress:function(g){this.progress=0;this.progressStep=g},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon")}else{f.error("An error occurred :(")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred :(")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Enter paths relative to Galaxy root",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Select folders or files to import",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){$("#jstree_browser").jstree("destroy");var l=$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var l=this.modal.$el.find(".link-checkbox").is(":checked");var k=$("textarea#import_paths").val();if(!k){f.info("Please enter a path relative to Galaxy root")}else{this.modal.disableButton("Import");k=k.split("\n");var j=[];for(var h=k.length-1;h>=0;h--){trimmed=k[h].trim();if(trimmed.length!==0){j.push(trimmed)}}this.initChainCallControl(j.length);this.chainCallImportingFolders(j,g,l,"admin_path")}},initChainCallControl:function(g){var h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));this.progress=0;this.progressStep=100/g;this.options.chain_call_control.total_number=g;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(l){var h=$("#jstree_browser").jstree().get_selected(true);var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var n=[];if(h.length<1){f.info("You have to select some items first")}else{this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;for(var j=h.length-1;j>=0;j--){if(h[j].li_attr.full_path!==undefined){n.push(h[j].li_attr.full_path)}}var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/n.length;this.progress=0;this.options.chain_call_control.total_number=n.length;var k=h[0].type;if(k==="folder"){this.chainCallImportingFolders(n,g,o,"userdir_folder")}else{if(k==="file"){this.chainCallImportingUserdirFiles(n)}}}},chainCallImportingUserdirFiles:function(j){var g=this;var h=j.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}return true}var i=$.when($.post("/api/libraries/datasets?encoded_folder_id="+g.id+"&source=userdir_file&path="+h));i.done(function(k){g.updateProgress();g.chainCallImportingUserdirFiles(j)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingUserdirFiles(j)})},chainCallImportingFolders:function(l,g,m,j){var h=this;var i=l.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}}var k=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+j+"&path="+i+"&preserve_dirs="+g+"&link_data="+m));k.done(function(n){h.updateProgress();h.chainCallImportingFolders(l,g,m,j)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(l,g,m,j)})},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");if(l.length<1){f.info("You have to select some datasets first")}else{this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/g.length;this.progress=0;var k=[];for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.options.chain_call_control.total_number=k.length;this.chainCallAddingHdas(k)}},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push("   <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push('   <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li class="divider"></li>');tmpl_array.push('        <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push("<% } else { %>");tmpl_array.push('     <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div id="jstree_browser">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history:  ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push('   <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","libs/jquery/jstree","mvc/library/library-model"],function(c,e,f,b,d){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}else{f.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var g=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new d.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";g.push(m)}this.options.chain_call_control.total_number=g.length;jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCall(g,n)},chainCall:function(h,k){var g=this;var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCall(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCall(h,k)})},initProgress:function(g){this.progress=0;this.progressStep=g},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon")}else{f.error("An error occurred :(")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred :(")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Enter paths relative to Galaxy root",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Select folders or files to import",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){$("#jstree_browser").jstree("destroy");var l=$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var l=this.modal.$el.find(".link-checkbox").is(":checked");var k=$("textarea#import_paths").val();if(!k){f.info("Please enter a path relative to Galaxy root")}else{this.modal.disableButton("Import");k=k.split("\n");var j=[];for(var h=k.length-1;h>=0;h--){trimmed=k[h].trim();if(trimmed.length!==0){j.push(trimmed)}}this.initChainCallControl(j.length);this.chainCallImportingFolders(j,g,l,"admin_path")}},initChainCallControl:function(g){var h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));this.progress=0;this.progressStep=100/g;this.options.chain_call_control.total_number=g;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(l){var h=$("#jstree_browser").jstree().get_selected(true);var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var n=[];if(h.length<1){f.info("You have to select some items first")}else{this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;for(var j=h.length-1;j>=0;j--){if(h[j].li_attr.full_path!==undefined){n.push(h[j].li_attr.full_path)}}var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/n.length;this.progress=0;this.options.chain_call_control.total_number=n.length;var k=h[0].type;if(k==="folder"){this.chainCallImportingFolders(n,g,o,"userdir_folder")}else{if(k==="file"){this.chainCallImportingUserdirFiles(n)}}}},chainCallImportingUserdirFiles:function(j){var g=this;var h=j.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}return true}var i=$.when($.post("/api/libraries/datasets?encoded_folder_id="+g.id+"&source=userdir_file&path="+h));i.done(function(k){g.updateProgress();g.chainCallImportingUserdirFiles(j)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingUserdirFiles(j)})},chainCallImportingFolders:function(l,g,m,j){var h=this;var i=l.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}return true}var k=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+j+"&path="+i+"&preserve_dirs="+g+"&link_data="+m));k.done(function(n){h.updateProgress();h.chainCallImportingFolders(l,g,m,j)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(l,g,m,j)})},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");if(l.length<1){f.info("You have to select some datasets first")}else{this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/g.length;this.progress=0;var k=[];for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.options.chain_call_control.total_number=k.length;this.chainCallAddingHdas(k)}},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push("   <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push('   <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li class="divider"></li>');tmpl_array.push('        <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push("<% } else { %>");tmpl_array.push('     <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div id="jstree_browser">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history:  ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push('   <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file

diff -r 3497f7509b007b04a4db905daf3509f1f3c76626 -r aec146e3828b16812ca24c5f8651ba3d0d483a6a static/scripts/packed/mvc/library/library-library-view.js
--- a/static/scripts/packed/mvc/library/library-library-view.js
+++ b/static/scripts/packed/mvc/library/library-library-view.js
@@ -1,1 +1,1 @@
-define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchLibrary()}},fetchLibrary:function(e){this.options=_.extend(this.options,e);this.model=new c.Library({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateLibrary();this.$el.html(f({item:this.model}));$("#center [data-toggle]").tooltip()},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_library_role_list.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateLibraryPermissions();this.$el.html(g({library:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while fetching library permissions. :(")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(i){this.options=_.extend(this.options,i);var e=this.options.fetched_permissions;var g=this;var f=this._serializeRoles(e.access_library_role_list);var j=this._serializeRoles(e.add_library_item_role_list);var h=this._serializeRoles(e.manage_library_role_list);var k=this._serializeRoles(e.modify_library_role_list);g.accessSelectObject=new a.View(this._createSelectOptions(this,"access_perm",f,true));g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",j,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",h,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",k,false))},_createSelectOptions:function(f,k,i,e){e=e===true?e:false;var j={minimumInputLength:0,css:k,multiple:true,placeholder:"Click to select a role",container:f.$el.find("#"+k),ajax:{url:"/api/libraries/"+f.id+"/permissions?scope=available&is_library_access="+e,dataType:"json",quietMillis:100,data:function(l,m){return{q:l,page_limit:10,page:m}},results:function(n,m){var l=(m*10)<n.total;return{results:n.roles,more:l}}},formatResult:function g(l){return l.name+" type: "+l.type},formatSelection:function h(l){return l.name},initSelection:function(l,n){var m=[];$(l.val().split(",")).each(function(){var o=this.split(":");m.push({id:o[1],name:o[1]})});n(m)},initialData:i.join(","),dropdownCssClass:"bigdrop"};return j},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var i=this._extractIds(this.accessSelectObject.$el.select2("data"));var e=this._extractIds(this.addSelectObject.$el.select2("data"));var j=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/libraries/"+g.id+"/permissions?action=set_permissions",{"access_ids[]":i,"add_ids[]":e,"manage_ids[]":j,"modify_ids[]":f,}).done(function(k){g.showPermissions({fetched_permissions:k});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting library permissions :(")})},templateLibrary:function(){var e=[];e.push('<div class="library_style_container">');e.push('  <div id="library_toolbar">');e.push('   <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push('   <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push('   <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push("  </div>");e.push("  <p>");e.push("  This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push('  <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push("  </p>");e.push('<div class="dataset_table">');e.push('   <table class="grid table table-striped table-condensed">');e.push("       <tr>");e.push('           <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push('           <td><%= _.escape(item.get("name")) %></td>');e.push("       </tr>");e.push('   <% if (item.get("file_ext")) { %>');e.push("       <tr>");e.push('           <th scope="row">Data type</th>');e.push('           <td><%= _.escape(item.get("file_ext")) %></td>');e.push("       </tr>");e.push("   <% } %>");e.push("    </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateLibraryPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push('  <div id="library_toolbar">');e.push('   <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>');e.push("  </div>");e.push('<h1>Library: <%= _.escape(library.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library permissions</h2>");e.push("<h4>Roles that can access the library</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on this library</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>');e.push("<h4>Roles that can add items to this library</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this library (folders and datasets).</div>');e.push("<h4>Roles that can modify this library</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{LibraryView:b}});
\ No newline at end of file
+define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchLibrary()}},fetchLibrary:function(e){this.options=_.extend(this.options,e);this.model=new c.Library({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateLibrary();this.$el.html(f({item:this.model}));$("#center [data-toggle]").tooltip()},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_library_role_list.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateLibraryPermissions();this.$el.html(g({library:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while fetching library permissions. :(")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f][1]+":"+g[f][0])}return e},prepareSelectBoxes:function(i){this.options=_.extend(this.options,i);var e=this.options.fetched_permissions;var g=this;var f=this._serializeRoles(e.access_library_role_list);var j=this._serializeRoles(e.add_library_item_role_list);var h=this._serializeRoles(e.manage_library_role_list);var k=this._serializeRoles(e.modify_library_role_list);g.accessSelectObject=new a.View(this._createSelectOptions(this,"access_perm",f,true));g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",j,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",h,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",k,false))},_createSelectOptions:function(f,k,i,e){e=e===true?e:false;var j={minimumInputLength:0,css:k,multiple:true,placeholder:"Click to select a role",container:f.$el.find("#"+k),ajax:{url:"/api/libraries/"+f.id+"/permissions?scope=available&is_library_access="+e,dataType:"json",quietMillis:100,data:function(l,m){return{q:l,page_limit:10,page:m}},results:function(n,m){var l=(m*10)<n.total;return{results:n.roles,more:l}}},formatResult:function g(l){return l.name+" type: "+l.type},formatSelection:function h(l){return l.name},initSelection:function(l,n){var m=[];$(l.val().split(",")).each(function(){var o=this.split(":");m.push({id:o[0],name:o[1]})});n(m)},initialData:i,dropdownCssClass:"bigdrop"};return j},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var i=this._extractIds(this.accessSelectObject.$el.select2("data"));var e=this._extractIds(this.addSelectObject.$el.select2("data"));var j=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/libraries/"+g.id+"/permissions?action=set_permissions",{"access_ids[]":i,"add_ids[]":e,"manage_ids[]":j,"modify_ids[]":f,}).done(function(k){g.showPermissions({fetched_permissions:k});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting library permissions :(")})},templateLibrary:function(){var e=[];e.push('<div class="library_style_container">');e.push('  <div id="library_toolbar">');e.push('   <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push('   <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push('   <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push("  </div>");e.push("  <p>");e.push("  This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push('  <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push("  </p>");e.push('<div class="dataset_table">');e.push('   <table class="grid table table-striped table-condensed">');e.push("       <tr>");e.push('           <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push('           <td><%= _.escape(item.get("name")) %></td>');e.push("       </tr>");e.push('   <% if (item.get("file_ext")) { %>');e.push("       <tr>");e.push('           <th scope="row">Data type</th>');e.push('           <td><%= _.escape(item.get("file_ext")) %></td>');e.push("       </tr>");e.push("   <% } %>");e.push("    </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateLibraryPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push('  <div id="library_toolbar">');e.push('   <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>');e.push("  </div>");e.push('<h1>Library: <%= _.escape(library.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library permissions</h2>");e.push("<h4>Roles that can access the library</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on this library</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>');e.push("<h4>Roles that can add items to this library</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this library (folders and datasets).</div>');e.push("<h4>Roles that can modify this library</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{LibraryView:b}});
\ No newline at end of file


https://bitbucket.org/galaxy/galaxy-central/commits/f163dd7c2ccd/
Changeset:   f163dd7c2ccd
User:        martenson
Date:        2014-09-16 22:02:12+00:00
Summary:     jstree refactoring, removed from global space, documentation to library imports, general JS cleanup
Affected #:  7 files

diff -r aec146e3828b16812ca24c5f8651ba3d0d483a6a -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 client/galaxy/scripts/libs/jquery/jstree.js
--- a/client/galaxy/scripts/libs/jquery/jstree.js
+++ b/client/galaxy/scripts/libs/jquery/jstree.js
@@ -2,7 +2,7 @@
 (function (factory) {
 	"use strict";
 	if (typeof define === 'function' && define.amd) {
-		// define(['jquery'], factory);
+		define(['jquery'], factory);
 	}
 	else if(typeof exports === 'object') {
 		factory(require('jquery'));

diff -r aec146e3828b16812ca24c5f8651ba3d0d483a6a -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -2,13 +2,11 @@
     "galaxy.masthead",
     "utils/utils",
     "libs/toastr",
-    "libs/jquery/jstree",
     "mvc/library/library-model"],
-function(mod_masthead,
+function( mod_masthead,
          mod_utils,
          mod_toastr,
-         ignore_jstree,
-         mod_library_model) {
+         mod_library_model ) {
 
 var FolderToolbarView = Backbone.View.extend({
   el: '#center',
@@ -40,7 +38,7 @@
   histories : null,
 
   initialize: function(options){
-    this.options = _.defaults(options || {}, this.defaults);
+    this.options = _.defaults( options || {}, this.defaults );
     this.render();
   },
 
@@ -202,89 +200,42 @@
    * Import all selected datasets into history.
    */
   importAllIntoHistory : function (){
-      this.modal.disableButton('Import');
-
-      // init the control counters
-      this.options.chain_call_control.total_number = 0;
-      this.options.chain_call_control.failed_number = 0;
-
-      var history_id = $("select[name=dataset_import_bulk] option:selected").val();
-      // we can save last used history to pre-select it next time
-      this.options.last_used_history_id = history_id;
-      var history_name = $("select[name=dataset_import_bulk] option:selected").text();
-
-      var dataset_ids = [];
-      $('#folder_table').find(':checked').each(function(){
-          if (this.parentElement.parentElement.id !== '') {
-              dataset_ids.push(this.parentElement.parentElement.id);
-          }
-      });
-      var progress_bar_tmpl = this.templateImportIntoHistoryProgressBar();
-      this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ history_name : history_name }));
-
-      // init the progress bar
-      var progressStep = 100 / dataset_ids.length;
-      this.initProgress(progressStep);
-
-      // prepare the dataset objects to be imported
-      var datasets_to_import = [];
-      for (var i = dataset_ids.length - 1; i >= 0; i--) {
-          var library_dataset_id = dataset_ids[i];
-          var historyItem = new mod_library_model.HistoryItem();
-          historyItem.url = historyItem.urlRoot + history_id + '/contents';
-          historyItem.content = library_dataset_id;
-          historyItem.source = 'library';
-          datasets_to_import.push(historyItem);
-      }
-      this.options.chain_call_control.total_number = datasets_to_import.length;
-
-      // set the used history as current so user will see the last one 
-      // that he imported into in the history panel on the 'analysis' page
-      jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + history_id  );
-
-      // call the recursive function to call ajax one after each other (request FIFO queue)
-      this.chainCall(datasets_to_import, history_name);
+    this.modal.disableButton('Import');
+    var history_id = $("select[name=dataset_import_bulk] option:selected").val();
+    var history_name = $("select[name=dataset_import_bulk] option:selected").text();
+    // we can save last used history to pre-select it next time
+    this.options.last_used_history_id = history_id;
+    var dataset_ids = [];
+    $('#folder_table').find(':checked').each(function(){
+        if (this.parentElement.parentElement.id !== '') {
+            dataset_ids.push(this.parentElement.parentElement.id);
+        }
+    });
+    // prepare the dataset objects to be imported
+    var datasets_to_import = [];
+    for (var i = dataset_ids.length - 1; i >= 0; i--) {
+        var library_dataset_id = dataset_ids[i];
+        var historyItem = new mod_library_model.HistoryItem();
+        historyItem.url = historyItem.urlRoot + history_id + '/contents';
+        historyItem.content = library_dataset_id;
+        historyItem.source = 'library';
+        datasets_to_import.push(historyItem);
+    }
+    this.initChainCallControl( { length: datasets_to_import.length, action: 'to_history', history_name: history_name } );
+    // set the used history as current so user will see the last one 
+    // that he imported into in the history panel on the 'analysis' page
+    jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + history_id  );
+    this.chainCallImportingIntoHistory( datasets_to_import, history_name );
   },
 
-  chainCall: function(history_item_set, history_name){
-    var self = this;
-    var popped_item = history_item_set.pop();
-    if (typeof popped_item === "undefined") {
-      if (this.options.chain_call_control.failed_number === 0){
-        mod_toastr.success('Selected datasets imported into history. Click this to start analysing it.', '', {onclick: function() {window.location='/'}});
-      } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
-        mod_toastr.error('There was an error and no datasets were imported into history.');
-      } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
-        mod_toastr.warning('Some of the datasets could not be imported into history. Click this to see what was imported.', '', {onclick: function() {window.location='/'}});
-      }
-      Galaxy.modal.hide();
-      return;
-    }
-    var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source}));
-
-    promise.done(function(){
-              // we are fine
-              self.updateProgress();
-              self.chainCall(history_item_set, history_name);
-            })
-            .fail(function(){
-              // we have a problem
-              self.options.chain_call_control.failed_number += 1;
-              self.updateProgress();
-              self.chainCall(history_item_set, history_name);
-            });
-  },
-
-  initProgress: function(progressStep){
-      this.progress = 0;
-      this.progressStep = progressStep;
-  },
-
+  /**
+   * Update the progress bar in modal window.
+   */
   updateProgress: function(){
       this.progress += this.progressStep;
-      $('.progress-bar-import').width(Math.round(this.progress) + '%');
-      txt_representation = Math.round(this.progress) + '% Complete';
-      $('.completion_span').text(txt_representation);
+      $( '.progress-bar-import' ).width( Math.round( this.progress ) + '%' );
+      txt_representation = Math.round( this.progress ) + '% Complete';
+      $( '.completion_span' ).text( txt_representation );
   },
 
   /**
@@ -292,16 +243,16 @@
    * @param  {str} folder_id id of the current folder
    * @param  {str} format    requested archive format
    */
-  download : function(folder_id, format){
+  download : function( folder_id, format ){
     var dataset_ids = [];
-        $('#folder_table').find(':checked').each(function(){
-            if (this.parentElement.parentElement.id !== '') {
-                dataset_ids.push(this.parentElement.parentElement.id);
+        $( '#folder_table' ).find( ':checked' ).each( function(){
+            if ( this.parentElement.parentElement.id !== '' ) {
+                dataset_ids.push( this.parentElement.parentElement.id );
             }
-        });
+        } );
     var url = '/api/libraries/datasets/download/' + format;
-    var data = {'ldda_ids' : dataset_ids};
-    this.processDownload(url, data, 'get');
+    var data = { 'ldda_ids' : dataset_ids };
+    this.processDownload( url, data, 'get' );
   },
 
   /**
@@ -311,27 +262,27 @@
    * @param  {obj} data   data to include in the request
    * @param  {str} method method of the request
    */
-  processDownload: function(url, data, method){
+  processDownload: function( url, data, method ){
     if ( url && data ){
       // data can be string of parameters or array/object
-      data = typeof data === 'string' ? data : $.param(data);
+      data = typeof data === 'string' ? data : $.param( data );
       // split params into form inputs
       var inputs = '';
-      $.each(data.split('&'), function(){
-              var pair = this.split('=');
+      $.each( data.split( '&' ), function(){
+              var pair = this.split( '=' );
               inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
       });
       // send request
       $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
-      .appendTo('body').submit().remove();
-      mod_toastr.info('Your download will begin soon');
+      .appendTo( 'body' ).submit().remove();
+      mod_toastr.info( 'Your download will begin soon' );
     } else {
-      mod_toastr.error('An error occurred :(');
+      mod_toastr.error( 'An error occurred :(' );
     }
   },
 
   addFilesFromHistoryModal: function(){
-    this.refreshUserHistoriesList(function(self){
+    this.refreshUserHistoriesList( function( self ){
       self.modal = Galaxy.modal;
       var template_modal = self.templateAddFilesFromHistory();
       var folder_name = self.options.full_path[self.options.full_path.length - 1][1]
@@ -355,7 +306,7 @@
           self.fetchAndDisplayHistoryContents(event.target.value);
         });
       } else {
-        mod_toastr.error('An error ocurred :(');
+        mod_toastr.error( 'An error ocurred :(' );
       }
     });
   },
@@ -438,23 +389,28 @@
     this.jstree.url = this.jstree.urlRoot + '?target=userdir&format=jstree&disable=' + disabled_jstree_element;
     this.jstree.fetch({
       success: function(model, response){
-        $('#jstree_browser').jstree("destroy");
-        var jstreeObject = $('#jstree_browser').jstree({
-          'core':{
-            'data': model
-          },
-          'plugins': ['types', 'checkbox'],
-          'types': {
-            "folder": {
-              "icon": "jstree-folder"
+        // This is to prevent double jquery load. I think. Carl is magician.
+        define( 'jquery', function(){ return jQuery; });
+        // Now we need jstree, time to lazy load it.
+        require([ 'libs/jquery/jstree' ], function(jstree){
+          $('#jstree_browser').jstree("destroy");
+          $('#jstree_browser').jstree({
+            'core':{
+              'data': model
             },
-            "file": {
-              "icon": "jstree-file"
+            'plugins': ['types', 'checkbox'],
+            'types': {
+              "folder": {
+                "icon": "jstree-folder"
+              },
+              "file": {
+                "icon": "jstree-file"
+              }
+            },
+            'checkbox': {
+              three_state: false
             }
-          },
-          'checkbox': {
-            three_state: false
-          }
+          });
         });
       },
       error: function(model, response){
@@ -476,19 +432,19 @@
     var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
     var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
     var paths = $('textarea#import_paths').val();
+    var valid_paths = [];
     if (!paths){
       mod_toastr.info('Please enter a path relative to Galaxy root');
     } else {
       this.modal.disableButton('Import');
       paths = paths.split('\n');
-      var valid_paths = [];
       for (var i = paths.length - 1; i >= 0; i--) {
         trimmed = paths[i].trim();
         if (trimmed.length!==0){
           valid_paths.push(trimmed);
         }
       };
-      this.initChainCallControl(valid_paths.length);
+      this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
       this.chainCallImportingFolders(valid_paths, preserve_dirs, link_data, 'admin_path');
     }
   },
@@ -496,87 +452,178 @@
   /**
    * Initialize the control of chaining requests
    * in the current modal.
+   * @param {int} length The number of items in the chain call.
    */
-  initChainCallControl: function(length){
-    var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-    this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
+  initChainCallControl: function( options ){
+    var template;
+    switch( options.action ){
+      case "adding_datasets":
+        template = this.templateAddingDatasetsProgressBar();
+        this.modal.$el.find( '.modal-body' ).html( template( { folder_name : this.options.folder_name } ) );
+        break;
+      case "deleting_datasets":
+        template = this.templateDeletingDatasetsProgressBar();
+        this.modal.$el.find( '.modal-body' ).html( template() );
+        break;
+      case "to_history":
+        template = this.templateImportIntoHistoryProgressBar();
+        this.modal.$el.find( '.modal-body' ).html( template( { history_name : options.history_name } ) );
+        break;
+      default:
+        console.error( 'Wrong action specified.')
+        break;
+    }
+
+    // var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
+    // this.modal.$el.find( '.modal-body' ).html( progress_bar_tmpl( { folder_name : this.options.folder_name } ) );
     this.progress = 0;
-    this.progressStep = 100 / length;
-    this.options.chain_call_control.total_number = length;
+    this.progressStep = 100 / options.length;
+    this.options.chain_call_control.total_number = options.length;
     this.options.chain_call_control.failed_number = 0;
   },
 
   /**
    * Take the selected items from the jstree, create a request queue
    * and send them one by one to the server for importing into 
-   * the current folder.
+   * the current folder. 
+   * 
+   * jstree.js has to be loaded before
+   * @see renderJstree
    */
-  importFromUserdirClicked: function (that){
-    var selected_nodes = $('#jstree_browser').jstree().get_selected(true);
-    var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
-    var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
+  importFromUserdirClicked: function ( that ){
+    var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
+    var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
+    var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
+    var selection_type = selected_nodes[0].type;
     var paths = [];
-    if (selected_nodes.length < 1){
-      mod_toastr.info('You have to select some items first');
+    if ( selected_nodes.length < 1 ){
+      mod_toastr.info( 'You have to select some items first' );
     } else {
-      // disable the button to prevent multiple submission
-      this.modal.disableButton('Import');
-      // init the chain control counters
-      this.options.chain_call_control.total_number = 0;
-      this.options.chain_call_control.failed_number = 0;
-
-      for (var i = selected_nodes.length - 1; i >= 0; i--){
-        if(selected_nodes[i].li_attr.full_path !== undefined){
-          paths.push(selected_nodes[i].li_attr.full_path);
+      this.modal.disableButton( 'Import' );
+      for ( var i = selected_nodes.length - 1; i >= 0; i-- ){
+        if ( selected_nodes[i].li_attr.full_path !== undefined ){
+          paths.push( selected_nodes[i].li_attr.full_path );
         }
       }
-      var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-      this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
-
-      // init the progress bar
-      this.progressStep = 100 / paths.length;
-      this.progress = 0;
-      this.options.chain_call_control.total_number = paths.length;
-      
-      var selection_type = selected_nodes[0].type;
-      // call the recursive function to call ajax one after each other (request FIFO queue)
-      if (selection_type === 'folder'){
-        this.chainCallImportingFolders(paths, preserve_dirs, link_data, 'userdir_folder');
-      } else if (selection_type === 'file'){
-        this.chainCallImportingUserdirFiles(paths);
+      this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } );
+      if ( selection_type === 'folder' ){
+        this.chainCallImportingFolders( paths, preserve_dirs, link_data, 'userdir_folder' );
+      } else if ( selection_type === 'file' ){
+        this.chainCallImportingUserdirFiles( paths );
       }
     }
   },
 
+  fetchAndDisplayHistoryContents: function(history_id){
+    var history_contents = new mod_library_model.HistoryContents({id:history_id});
+    var self = this;
+    history_contents.fetch({
+      success: function(history_contents){
+        var history_contents_template = self.templateHistoryContents();
+        self.histories.get(history_id).set({'contents' : history_contents});
+        self.modal.$el.find('#selected_history_content').html(history_contents_template({history_contents: history_contents.models.reverse()}));
+      },
+      error: function(model, response){
+        if (typeof response.responseJSON !== "undefined"){
+          mod_toastr.error(response.responseJSON.err_msg);
+        } else {
+          mod_toastr.error('An error ocurred :(');
+        }
+      }
+    });
+  },
+
+  /**
+   * Import all selected datasets from history into the current folder.
+   */
+  addAllDatasetsFromHistory : function (){
+    var checked_hdas = this.modal.$el.find( '#selected_history_content' ).find( ':checked' );
+    var history_dataset_ids = [];
+    var hdas_to_add = [];
+    if ( checked_hdas.length < 1 ){
+      mod_toastr.info( 'You have to select some datasets first' );
+    } else {
+      this.modal.disableButton( 'Add' );
+      checked_hdas.each(function(){
+        var hid = $( this.parentElement ).data( 'id' );
+          if ( hid ) {
+            history_dataset_ids.push( hid );
+          }
+      });
+      for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) {
+        history_dataset_id = history_dataset_ids[i];
+        var folder_item = new mod_library_model.Item();
+        folder_item.url = '/api/folders/' + this.options.id + '/contents';
+        folder_item.set( { 'from_hda_id':history_dataset_id } );
+        hdas_to_add.push( folder_item );
+      }
+      this.initChainCallControl( { length: hdas_to_add.length, action: 'adding_datasets' } );
+      this.chainCallAddingHdas( hdas_to_add );
+    }
+  },
+
+  /**
+   * Take array of empty history items and make request for each of them
+   * to create it on server. Update progress in between calls.
+   * @param  {array} history_item_set array of empty history items
+   * @param  {str} history_name     name of the history to import to
+   */
+  chainCallImportingIntoHistory: function( history_item_set, history_name ){
+    var self = this;
+    var popped_item = history_item_set.pop();
+    if ( typeof popped_item == "undefined" ) {
+      if ( this.options.chain_call_control.failed_number === 0 ){
+        mod_toastr.success( 'Selected datasets imported into history. Click this to start analysing it.', '', { onclick: function() { window.location='/' } } );
+      } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
+        mod_toastr.error( 'There was an error and no datasets were imported into history.' );
+      } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
+        mod_toastr.warning( 'Some of the datasets could not be imported into history. Click this to see what was imported.', '', { onclick: function() { window.location='/' } } );
+      }
+      Galaxy.modal.hide();
+      return true;
+    }
+    var promise = $.when( popped_item.save( { content: popped_item.content, source: popped_item.source } ) );
+
+    promise.done( function(){
+              self.updateProgress();
+              self.chainCallImportingIntoHistory( history_item_set, history_name );
+            } )
+            .fail( function(){
+              self.options.chain_call_control.failed_number += 1;
+              self.updateProgress();
+              self.chainCallImportingIntoHistory( history_item_set, history_name );
+            } );
+  },
+
   /**
    * Take the array of paths and createa request for each of them
    * calling them in chain. Update the progress bar in between each.
    * @param  {array} paths           paths relative to user folder on Galaxy
    */
-  chainCallImportingUserdirFiles: function(paths){
+  chainCallImportingUserdirFiles: function( paths ){
     var that = this;
     var popped_item = paths.pop();
-    if (typeof popped_item === "undefined") {
-      if (this.options.chain_call_control.failed_number === 0){
-        mod_toastr.success('Selected files imported into the current folder');
+    if ( typeof popped_item === "undefined" ) {
+      if ( this.options.chain_call_control.failed_number === 0 ){
+        mod_toastr.success( 'Selected files imported into the current folder' );
         Galaxy.modal.hide();
       } else {
-        mod_toastr.error('Something went wrong :(');
+        mod_toastr.error( 'Something went wrong :(' );
       }
       return true;
     }
-    var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id + 
+    var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + 
                                                        '&source=userdir_file' +
-                                                       '&path=' + popped_item))
-    promise.done(function(response){
+                                                       '&path=' + popped_item ) )
+    promise.done( function( response ){
               that.updateProgress();
-              that.chainCallImportingUserdirFiles(paths);
-            })
-            .fail(function(){
+              that.chainCallImportingUserdirFiles( paths );
+            } )
+            .fail( function(){
               that.options.chain_call_control.failed_number += 1;
               that.updateProgress();
-              that.chainCallImportingUserdirFiles(paths);
-            });
+              that.chainCallImportingUserdirFiles( paths );
+            } );
   },
 
   /**
@@ -618,98 +665,80 @@
             });
   },
 
-  fetchAndDisplayHistoryContents: function(history_id){
-    var history_contents = new mod_library_model.HistoryContents({id:history_id});
-    var self = this;
-    history_contents.fetch({
-      success: function(history_contents){
-        var history_contents_template = self.templateHistoryContents();
-        self.histories.get(history_id).set({'contents' : history_contents});
-        self.modal.$el.find('#selected_history_content').html(history_contents_template({history_contents: history_contents.models.reverse()}));
-      },
-      error: function(model, response){
-        if (typeof response.responseJSON !== "undefined"){
-          mod_toastr.error(response.responseJSON.err_msg);
-        } else {
-          mod_toastr.error('An error ocurred :(');
-        }
-      }
-    });
-  },
-
-  // add all selected datasets from history into current folder
-  addAllDatasetsFromHistory : function (){
-    var checked_hdas = this.modal.$el.find('#selected_history_content').find(':checked');
-      if (checked_hdas.length < 1){
-        mod_toastr.info('You have to select some datasets first');
-      } else {
-        // disable the button to prevent multiple submission
-        this.modal.disableButton('Add');
-        // init the control counters
-        this.options.chain_call_control.total_number = 0;
-        this.options.chain_call_control.failed_number = 0;
-
-        var history_dataset_ids = [];
-        checked_hdas.each(function(){
-          var hid = $(this.parentElement).data('id');
-            if (hid) {
-                history_dataset_ids.push(hid);
-            }
-        });
-        var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-        this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
-
-        // init the progress bar
-        this.progressStep = 100 / history_dataset_ids.length;
-        this.progress = 0;
-
-        // prepare the dataset items to be added
-        var hdas_to_add = [];
-        for (var i = history_dataset_ids.length - 1; i >= 0; i--) {
-            history_dataset_id = history_dataset_ids[i];
-            var folder_item = new mod_library_model.Item();
-            folder_item.url = '/api/folders/' + this.options.id + '/contents';
-            folder_item.set({'from_hda_id':history_dataset_id});
-            hdas_to_add.push(folder_item);
-        }
-        this.options.chain_call_control.total_number = hdas_to_add.length;
-        // call the recursive function to call ajax one after each other (request FIFO queue)
-        this.chainCallAddingHdas(hdas_to_add);
-      }
-  },
-
-  chainCallAddingHdas: function(hdas_set){
+  /**
+   * Take the array of hdas and create a request for each. 
+   * Call them in chain and update progress bar in between each.
+   * @param  {array} hdas_set array of empty hda objects
+   */
+  chainCallAddingHdas: function( hdas_set ){
     var self = this;
     this.added_hdas = new mod_library_model.Folder();
     var popped_item = hdas_set.pop();
-    if (typeof popped_item === "undefined") {
-      if (this.options.chain_call_control.failed_number === 0){
-        mod_toastr.success('Selected datasets from history added to the folder');
-      } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
-        mod_toastr.error('There was an error and no datasets were added to the folder.');
-      } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
-        mod_toastr.warning('Some of the datasets could not be added to the folder');
+    if ( typeof popped_item == "undefined" ) {
+      if ( this.options.chain_call_control.failed_number === 0 ){
+        mod_toastr.success( 'Selected datasets from history added to the folder' );
+      } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
+        mod_toastr.error( 'There was an error and no datasets were added to the folder.' );
+      } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
+        mod_toastr.warning( 'Some of the datasets could not be added to the folder' );
       }
       Galaxy.modal.hide();
       return this.added_hdas;
     }
-    var promise = $.when(popped_item.save({from_hda_id: popped_item.get('from_hda_id')}));
+    var promise = $.when( popped_item.save( { from_hda_id: popped_item.get( 'from_hda_id' ) } ) );
 
-    promise.done(function(model){
-              // we are fine
-              Galaxy.libraries.folderListView.collection.add(model);
+    promise.done( function( model ){
+              Galaxy.libraries.folderListView.collection.add( model );
               self.updateProgress();
-              self.chainCallAddingHdas(hdas_set);
+              self.chainCallAddingHdas( hdas_set );
             })
-            .fail(function(){
-              // we have a problem
+            .fail( function(){
               self.options.chain_call_control.failed_number += 1;
               self.updateProgress();
-              self.chainCallAddingHdas(hdas_set);
+              self.chainCallAddingHdas( hdas_set );
             });
   },
 
   /**
+   * Take the array of lddas, create request for each and 
+   * call them in chain. Update progress bar in between each.
+   * @param  {array} lddas_set array of lddas to delete
+   */
+  chainCallDeletingHdas: function( lddas_set ){
+  var self = this;
+  this.deleted_lddas = new mod_library_model.Folder();
+  var popped_item = lddas_set.pop();
+  if ( typeof popped_item === "undefined" ) {
+    if ( this.options.chain_call_control.failed_number === 0 ){
+      mod_toastr.success( 'Selected datasets deleted' );
+    } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
+      mod_toastr.error( 'There was an error and no datasets were deleted.' );
+    } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
+      mod_toastr.warning( 'Some of the datasets could not be deleted' );
+    }
+    Galaxy.modal.hide();
+    return this.deleted_lddas;
+  }
+  var promise = $.when( popped_item.destroy() );
+
+  promise.done( function( dataset ){
+            Galaxy.libraries.folderListView.collection.remove( popped_item.id );
+            self.updateProgress();
+            // add the deleted dataset to collection, triggers rendering
+            if ( Galaxy.libraries.folderListView.options.include_deleted ){
+              var updated_dataset = new mod_library_model.Item( dataset );
+              Galaxy.libraries.folderListView.collection.add( updated_dataset );
+            }
+            self.chainCallDeletingHdas( lddas_set );
+          })
+          .fail( function(){
+            self.options.chain_call_control.failed_number += 1;
+            self.updateProgress();
+            self.chainCallDeletingHdas( lddas_set );
+          });
+  },
+
+  /**
    * Handles the click on 'show deleted' checkbox
    */
   checkIncludeDeleted: function(event){
@@ -765,43 +794,6 @@
     }
   },
 
-  chainCallDeletingHdas: function(lddas_set){
-  var self = this;
-  this.deleted_lddas = new mod_library_model.Folder();
-  var popped_item = lddas_set.pop();
-  if (typeof popped_item === "undefined") {
-    if (this.options.chain_call_control.failed_number === 0){
-      mod_toastr.success('Selected datasets deleted');
-    } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
-      mod_toastr.error('There was an error and no datasets were deleted.');
-    } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
-      mod_toastr.warning('Some of the datasets could not be deleted');
-    }
-    Galaxy.modal.hide();
-    return this.deleted_lddas;
-  }
-  var promise = $.when(popped_item.destroy());
-
-  promise.done(function(dataset){
-            // we are fine
-            Galaxy.libraries.folderListView.collection.remove(popped_item.id);
-            self.updateProgress();
-            // add the deleted dataset to collection, triggers rendering
-            if (Galaxy.libraries.folderListView.options.include_deleted){
-              var updated_dataset = new mod_library_model.Item(dataset);
-              Galaxy.libraries.folderListView.collection.add(updated_dataset);
-            }
-            // execute next request
-            self.chainCallDeletingHdas(lddas_set);
-          })
-          .fail(function(){
-            // we have a problem
-            self.options.chain_call_control.failed_number += 1;
-            self.updateProgress();
-            // execute next request
-            self.chainCallDeletingHdas(lddas_set);
-          });
-  },
 
   showLibInfo: function(){
     var library_id = Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;
@@ -989,7 +981,7 @@
     var tmpl_array = [];
 
     tmpl_array.push('<div class="import_text">');
-    tmpl_array.push('Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>');
+    tmpl_array.push('Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>');
     tmpl_array.push('</div>');
     tmpl_array.push('<div class="progress">');
     tmpl_array.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');

diff -r aec146e3828b16812ca24c5f8651ba3d0d483a6a -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 static/scripts/libs/jquery/jstree.js
--- a/static/scripts/libs/jquery/jstree.js
+++ b/static/scripts/libs/jquery/jstree.js
@@ -2,7 +2,7 @@
 (function (factory) {
 	"use strict";
 	if (typeof define === 'function' && define.amd) {
-		// define(['jquery'], factory);
+		define(['jquery'], factory);
 	}
 	else if(typeof exports === 'object') {
 		factory(require('jquery'));

diff -r aec146e3828b16812ca24c5f8651ba3d0d483a6a -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 static/scripts/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -2,13 +2,11 @@
     "galaxy.masthead",
     "utils/utils",
     "libs/toastr",
-    "libs/jquery/jstree",
     "mvc/library/library-model"],
-function(mod_masthead,
+function( mod_masthead,
          mod_utils,
          mod_toastr,
-         ignore_jstree,
-         mod_library_model) {
+         mod_library_model ) {
 
 var FolderToolbarView = Backbone.View.extend({
   el: '#center',
@@ -40,7 +38,7 @@
   histories : null,
 
   initialize: function(options){
-    this.options = _.defaults(options || {}, this.defaults);
+    this.options = _.defaults( options || {}, this.defaults );
     this.render();
   },
 
@@ -202,89 +200,42 @@
    * Import all selected datasets into history.
    */
   importAllIntoHistory : function (){
-      this.modal.disableButton('Import');
-
-      // init the control counters
-      this.options.chain_call_control.total_number = 0;
-      this.options.chain_call_control.failed_number = 0;
-
-      var history_id = $("select[name=dataset_import_bulk] option:selected").val();
-      // we can save last used history to pre-select it next time
-      this.options.last_used_history_id = history_id;
-      var history_name = $("select[name=dataset_import_bulk] option:selected").text();
-
-      var dataset_ids = [];
-      $('#folder_table').find(':checked').each(function(){
-          if (this.parentElement.parentElement.id !== '') {
-              dataset_ids.push(this.parentElement.parentElement.id);
-          }
-      });
-      var progress_bar_tmpl = this.templateImportIntoHistoryProgressBar();
-      this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ history_name : history_name }));
-
-      // init the progress bar
-      var progressStep = 100 / dataset_ids.length;
-      this.initProgress(progressStep);
-
-      // prepare the dataset objects to be imported
-      var datasets_to_import = [];
-      for (var i = dataset_ids.length - 1; i >= 0; i--) {
-          var library_dataset_id = dataset_ids[i];
-          var historyItem = new mod_library_model.HistoryItem();
-          historyItem.url = historyItem.urlRoot + history_id + '/contents';
-          historyItem.content = library_dataset_id;
-          historyItem.source = 'library';
-          datasets_to_import.push(historyItem);
-      }
-      this.options.chain_call_control.total_number = datasets_to_import.length;
-
-      // set the used history as current so user will see the last one 
-      // that he imported into in the history panel on the 'analysis' page
-      jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + history_id  );
-
-      // call the recursive function to call ajax one after each other (request FIFO queue)
-      this.chainCall(datasets_to_import, history_name);
+    this.modal.disableButton('Import');
+    var history_id = $("select[name=dataset_import_bulk] option:selected").val();
+    var history_name = $("select[name=dataset_import_bulk] option:selected").text();
+    // we can save last used history to pre-select it next time
+    this.options.last_used_history_id = history_id;
+    var dataset_ids = [];
+    $('#folder_table').find(':checked').each(function(){
+        if (this.parentElement.parentElement.id !== '') {
+            dataset_ids.push(this.parentElement.parentElement.id);
+        }
+    });
+    // prepare the dataset objects to be imported
+    var datasets_to_import = [];
+    for (var i = dataset_ids.length - 1; i >= 0; i--) {
+        var library_dataset_id = dataset_ids[i];
+        var historyItem = new mod_library_model.HistoryItem();
+        historyItem.url = historyItem.urlRoot + history_id + '/contents';
+        historyItem.content = library_dataset_id;
+        historyItem.source = 'library';
+        datasets_to_import.push(historyItem);
+    }
+    this.initChainCallControl( { length: datasets_to_import.length, action: 'to_history', history_name: history_name } );
+    // set the used history as current so user will see the last one 
+    // that he imported into in the history panel on the 'analysis' page
+    jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + history_id  );
+    this.chainCallImportingIntoHistory( datasets_to_import, history_name );
   },
 
-  chainCall: function(history_item_set, history_name){
-    var self = this;
-    var popped_item = history_item_set.pop();
-    if (typeof popped_item === "undefined") {
-      if (this.options.chain_call_control.failed_number === 0){
-        mod_toastr.success('Selected datasets imported into history. Click this to start analysing it.', '', {onclick: function() {window.location='/'}});
-      } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
-        mod_toastr.error('There was an error and no datasets were imported into history.');
-      } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
-        mod_toastr.warning('Some of the datasets could not be imported into history. Click this to see what was imported.', '', {onclick: function() {window.location='/'}});
-      }
-      Galaxy.modal.hide();
-      return;
-    }
-    var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source}));
-
-    promise.done(function(){
-              // we are fine
-              self.updateProgress();
-              self.chainCall(history_item_set, history_name);
-            })
-            .fail(function(){
-              // we have a problem
-              self.options.chain_call_control.failed_number += 1;
-              self.updateProgress();
-              self.chainCall(history_item_set, history_name);
-            });
-  },
-
-  initProgress: function(progressStep){
-      this.progress = 0;
-      this.progressStep = progressStep;
-  },
-
+  /**
+   * Update the progress bar in modal window.
+   */
   updateProgress: function(){
       this.progress += this.progressStep;
-      $('.progress-bar-import').width(Math.round(this.progress) + '%');
-      txt_representation = Math.round(this.progress) + '% Complete';
-      $('.completion_span').text(txt_representation);
+      $( '.progress-bar-import' ).width( Math.round( this.progress ) + '%' );
+      txt_representation = Math.round( this.progress ) + '% Complete';
+      $( '.completion_span' ).text( txt_representation );
   },
 
   /**
@@ -292,16 +243,16 @@
    * @param  {str} folder_id id of the current folder
    * @param  {str} format    requested archive format
    */
-  download : function(folder_id, format){
+  download : function( folder_id, format ){
     var dataset_ids = [];
-        $('#folder_table').find(':checked').each(function(){
-            if (this.parentElement.parentElement.id !== '') {
-                dataset_ids.push(this.parentElement.parentElement.id);
+        $( '#folder_table' ).find( ':checked' ).each( function(){
+            if ( this.parentElement.parentElement.id !== '' ) {
+                dataset_ids.push( this.parentElement.parentElement.id );
             }
-        });
+        } );
     var url = '/api/libraries/datasets/download/' + format;
-    var data = {'ldda_ids' : dataset_ids};
-    this.processDownload(url, data, 'get');
+    var data = { 'ldda_ids' : dataset_ids };
+    this.processDownload( url, data, 'get' );
   },
 
   /**
@@ -311,27 +262,27 @@
    * @param  {obj} data   data to include in the request
    * @param  {str} method method of the request
    */
-  processDownload: function(url, data, method){
+  processDownload: function( url, data, method ){
     if ( url && data ){
       // data can be string of parameters or array/object
-      data = typeof data === 'string' ? data : $.param(data);
+      data = typeof data === 'string' ? data : $.param( data );
       // split params into form inputs
       var inputs = '';
-      $.each(data.split('&'), function(){
-              var pair = this.split('=');
+      $.each( data.split( '&' ), function(){
+              var pair = this.split( '=' );
               inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
       });
       // send request
       $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
-      .appendTo('body').submit().remove();
-      mod_toastr.info('Your download will begin soon');
+      .appendTo( 'body' ).submit().remove();
+      mod_toastr.info( 'Your download will begin soon' );
     } else {
-      mod_toastr.error('An error occurred :(');
+      mod_toastr.error( 'An error occurred :(' );
     }
   },
 
   addFilesFromHistoryModal: function(){
-    this.refreshUserHistoriesList(function(self){
+    this.refreshUserHistoriesList( function( self ){
       self.modal = Galaxy.modal;
       var template_modal = self.templateAddFilesFromHistory();
       var folder_name = self.options.full_path[self.options.full_path.length - 1][1]
@@ -355,7 +306,7 @@
           self.fetchAndDisplayHistoryContents(event.target.value);
         });
       } else {
-        mod_toastr.error('An error ocurred :(');
+        mod_toastr.error( 'An error ocurred :(' );
       }
     });
   },
@@ -438,23 +389,28 @@
     this.jstree.url = this.jstree.urlRoot + '?target=userdir&format=jstree&disable=' + disabled_jstree_element;
     this.jstree.fetch({
       success: function(model, response){
-        $('#jstree_browser').jstree("destroy");
-        var jstreeObject = $('#jstree_browser').jstree({
-          'core':{
-            'data': model
-          },
-          'plugins': ['types', 'checkbox'],
-          'types': {
-            "folder": {
-              "icon": "jstree-folder"
+        // This is to prevent double jquery load. I think. Carl is magician.
+        define( 'jquery', function(){ return jQuery; });
+        // Now we need jstree, time to lazy load it.
+        require([ 'libs/jquery/jstree' ], function(jstree){
+          $('#jstree_browser').jstree("destroy");
+          $('#jstree_browser').jstree({
+            'core':{
+              'data': model
             },
-            "file": {
-              "icon": "jstree-file"
+            'plugins': ['types', 'checkbox'],
+            'types': {
+              "folder": {
+                "icon": "jstree-folder"
+              },
+              "file": {
+                "icon": "jstree-file"
+              }
+            },
+            'checkbox': {
+              three_state: false
             }
-          },
-          'checkbox': {
-            three_state: false
-          }
+          });
         });
       },
       error: function(model, response){
@@ -476,19 +432,19 @@
     var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
     var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
     var paths = $('textarea#import_paths').val();
+    var valid_paths = [];
     if (!paths){
       mod_toastr.info('Please enter a path relative to Galaxy root');
     } else {
       this.modal.disableButton('Import');
       paths = paths.split('\n');
-      var valid_paths = [];
       for (var i = paths.length - 1; i >= 0; i--) {
         trimmed = paths[i].trim();
         if (trimmed.length!==0){
           valid_paths.push(trimmed);
         }
       };
-      this.initChainCallControl(valid_paths.length);
+      this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
       this.chainCallImportingFolders(valid_paths, preserve_dirs, link_data, 'admin_path');
     }
   },
@@ -496,127 +452,68 @@
   /**
    * Initialize the control of chaining requests
    * in the current modal.
+   * @param {int} length The number of items in the chain call.
    */
-  initChainCallControl: function(length){
-    var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-    this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
+  initChainCallControl: function( options ){
+    var template;
+    switch( options.action ){
+      case "adding_datasets":
+        template = this.templateAddingDatasetsProgressBar();
+        this.modal.$el.find( '.modal-body' ).html( template( { folder_name : this.options.folder_name } ) );
+        break;
+      case "deleting_datasets":
+        template = this.templateDeletingDatasetsProgressBar();
+        this.modal.$el.find( '.modal-body' ).html( template() );
+        break;
+      case "to_history":
+        template = this.templateImportIntoHistoryProgressBar();
+        this.modal.$el.find( '.modal-body' ).html( template( { history_name : options.history_name } ) );
+        break;
+      default:
+        console.error( 'Wrong action specified.')
+        break;
+    }
+
+    // var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
+    // this.modal.$el.find( '.modal-body' ).html( progress_bar_tmpl( { folder_name : this.options.folder_name } ) );
     this.progress = 0;
-    this.progressStep = 100 / length;
-    this.options.chain_call_control.total_number = length;
+    this.progressStep = 100 / options.length;
+    this.options.chain_call_control.total_number = options.length;
     this.options.chain_call_control.failed_number = 0;
   },
 
   /**
    * Take the selected items from the jstree, create a request queue
    * and send them one by one to the server for importing into 
-   * the current folder.
+   * the current folder. 
+   * 
+   * jstree.js has to be loaded before
+   * @see renderJstree
    */
-  importFromUserdirClicked: function (that){
-    var selected_nodes = $('#jstree_browser').jstree().get_selected(true);
-    var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
-    var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
+  importFromUserdirClicked: function ( that ){
+    var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
+    var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
+    var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
+    var selection_type = selected_nodes[0].type;
     var paths = [];
-    if (selected_nodes.length < 1){
-      mod_toastr.info('You have to select some items first');
+    if ( selected_nodes.length < 1 ){
+      mod_toastr.info( 'You have to select some items first' );
     } else {
-      // disable the button to prevent multiple submission
-      this.modal.disableButton('Import');
-      // init the chain control counters
-      this.options.chain_call_control.total_number = 0;
-      this.options.chain_call_control.failed_number = 0;
-
-      for (var i = selected_nodes.length - 1; i >= 0; i--){
-        if(selected_nodes[i].li_attr.full_path !== undefined){
-          paths.push(selected_nodes[i].li_attr.full_path);
+      this.modal.disableButton( 'Import' );
+      for ( var i = selected_nodes.length - 1; i >= 0; i-- ){
+        if ( selected_nodes[i].li_attr.full_path !== undefined ){
+          paths.push( selected_nodes[i].li_attr.full_path );
         }
       }
-      var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-      this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
-
-      // init the progress bar
-      this.progressStep = 100 / paths.length;
-      this.progress = 0;
-      this.options.chain_call_control.total_number = paths.length;
-      
-      var selection_type = selected_nodes[0].type;
-      // call the recursive function to call ajax one after each other (request FIFO queue)
-      if (selection_type === 'folder'){
-        this.chainCallImportingFolders(paths, preserve_dirs, link_data, 'userdir_folder');
-      } else if (selection_type === 'file'){
-        this.chainCallImportingUserdirFiles(paths);
+      this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } );
+      if ( selection_type === 'folder' ){
+        this.chainCallImportingFolders( paths, preserve_dirs, link_data, 'userdir_folder' );
+      } else if ( selection_type === 'file' ){
+        this.chainCallImportingUserdirFiles( paths );
       }
     }
   },
 
-  /**
-   * Take the array of paths and createa request for each of them
-   * calling them in chain. Update the progress bar in between each.
-   * @param  {array} paths           paths relative to user folder on Galaxy
-   */
-  chainCallImportingUserdirFiles: function(paths){
-    var that = this;
-    var popped_item = paths.pop();
-    if (typeof popped_item === "undefined") {
-      if (this.options.chain_call_control.failed_number === 0){
-        mod_toastr.success('Selected files imported into the current folder');
-        Galaxy.modal.hide();
-      } else {
-        mod_toastr.error('Something went wrong :(');
-      }
-      return true;
-    }
-    var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id + 
-                                                       '&source=userdir_file' +
-                                                       '&path=' + popped_item))
-    promise.done(function(response){
-              that.updateProgress();
-              that.chainCallImportingUserdirFiles(paths);
-            })
-            .fail(function(){
-              that.options.chain_call_control.failed_number += 1;
-              that.updateProgress();
-              that.chainCallImportingUserdirFiles(paths);
-            });
-  },
-
-  /**
-   * Take the array of paths and createa request for each of them
-   * calling them in chain. Update the progress bar in between each.
-   * @param  {array} paths           paths relative to Galaxy root folder
-   * @param  {boolean} preserve_dirs indicates whether to preserve folder structure
-   * @param  {boolean} link_data     copy files to Galaxy or link instead
-   * @param  {str} source            string representing what type of folder 
-   *                                 is the source of import
-   */
-  chainCallImportingFolders: function(paths, preserve_dirs, link_data, source){
-    // need to check which paths to call
-    var that = this;
-    var popped_item = paths.pop();
-    if (typeof popped_item == "undefined") {
-      if (this.options.chain_call_control.failed_number === 0){
-        mod_toastr.success('Selected folders and their contents imported into the current folder');
-        Galaxy.modal.hide();
-      } else {
-        mod_toastr.error('Something went wrong :(');
-      }
-      return true;
-    }
-    var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
-                                                      '&source=' + source +
-                                                      '&path=' + popped_item +
-                                                      '&preserve_dirs=' + preserve_dirs +
-                                                      '&link_data=' + link_data))
-    promise.done(function(response){
-              that.updateProgress();
-              that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
-            })
-            .fail(function(){
-              that.options.chain_call_control.failed_number += 1;
-              that.updateProgress();
-              that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
-            });
-  },
-
   fetchAndDisplayHistoryContents: function(history_id){
     var history_contents = new mod_library_model.HistoryContents({id:history_id});
     var self = this;
@@ -636,79 +533,212 @@
     });
   },
 
-  // add all selected datasets from history into current folder
+  /**
+   * Import all selected datasets from history into the current folder.
+   */
   addAllDatasetsFromHistory : function (){
-    var checked_hdas = this.modal.$el.find('#selected_history_content').find(':checked');
-      if (checked_hdas.length < 1){
-        mod_toastr.info('You have to select some datasets first');
-      } else {
-        // disable the button to prevent multiple submission
-        this.modal.disableButton('Add');
-        // init the control counters
-        this.options.chain_call_control.total_number = 0;
-        this.options.chain_call_control.failed_number = 0;
-
-        var history_dataset_ids = [];
-        checked_hdas.each(function(){
-          var hid = $(this.parentElement).data('id');
-            if (hid) {
-                history_dataset_ids.push(hid);
-            }
-        });
-        var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-        this.modal.$el.find('.modal-body').html(progress_bar_tmpl({ folder_name : this.options.folder_name }));
-
-        // init the progress bar
-        this.progressStep = 100 / history_dataset_ids.length;
-        this.progress = 0;
-
-        // prepare the dataset items to be added
-        var hdas_to_add = [];
-        for (var i = history_dataset_ids.length - 1; i >= 0; i--) {
-            history_dataset_id = history_dataset_ids[i];
-            var folder_item = new mod_library_model.Item();
-            folder_item.url = '/api/folders/' + this.options.id + '/contents';
-            folder_item.set({'from_hda_id':history_dataset_id});
-            hdas_to_add.push(folder_item);
-        }
-        this.options.chain_call_control.total_number = hdas_to_add.length;
-        // call the recursive function to call ajax one after each other (request FIFO queue)
-        this.chainCallAddingHdas(hdas_to_add);
+    var checked_hdas = this.modal.$el.find( '#selected_history_content' ).find( ':checked' );
+    var history_dataset_ids = [];
+    var hdas_to_add = [];
+    if ( checked_hdas.length < 1 ){
+      mod_toastr.info( 'You have to select some datasets first' );
+    } else {
+      this.modal.disableButton( 'Add' );
+      checked_hdas.each(function(){
+        var hid = $( this.parentElement ).data( 'id' );
+          if ( hid ) {
+            history_dataset_ids.push( hid );
+          }
+      });
+      for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) {
+        history_dataset_id = history_dataset_ids[i];
+        var folder_item = new mod_library_model.Item();
+        folder_item.url = '/api/folders/' + this.options.id + '/contents';
+        folder_item.set( { 'from_hda_id':history_dataset_id } );
+        hdas_to_add.push( folder_item );
       }
+      this.initChainCallControl( { length: hdas_to_add.length, action: 'adding_datasets' } );
+      this.chainCallAddingHdas( hdas_to_add );
+    }
   },
 
-  chainCallAddingHdas: function(hdas_set){
+  /**
+   * Take array of empty history items and make request for each of them
+   * to create it on server. Update progress in between calls.
+   * @param  {array} history_item_set array of empty history items
+   * @param  {str} history_name     name of the history to import to
+   */
+  chainCallImportingIntoHistory: function( history_item_set, history_name ){
+    var self = this;
+    var popped_item = history_item_set.pop();
+    if ( typeof popped_item == "undefined" ) {
+      if ( this.options.chain_call_control.failed_number === 0 ){
+        mod_toastr.success( 'Selected datasets imported into history. Click this to start analysing it.', '', { onclick: function() { window.location='/' } } );
+      } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
+        mod_toastr.error( 'There was an error and no datasets were imported into history.' );
+      } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
+        mod_toastr.warning( 'Some of the datasets could not be imported into history. Click this to see what was imported.', '', { onclick: function() { window.location='/' } } );
+      }
+      Galaxy.modal.hide();
+      return true;
+    }
+    var promise = $.when( popped_item.save( { content: popped_item.content, source: popped_item.source } ) );
+
+    promise.done( function(){
+              self.updateProgress();
+              self.chainCallImportingIntoHistory( history_item_set, history_name );
+            } )
+            .fail( function(){
+              self.options.chain_call_control.failed_number += 1;
+              self.updateProgress();
+              self.chainCallImportingIntoHistory( history_item_set, history_name );
+            } );
+  },
+
+  /**
+   * Take the array of paths and createa request for each of them
+   * calling them in chain. Update the progress bar in between each.
+   * @param  {array} paths           paths relative to user folder on Galaxy
+   */
+  chainCallImportingUserdirFiles: function( paths ){
+    var that = this;
+    var popped_item = paths.pop();
+    if ( typeof popped_item === "undefined" ) {
+      if ( this.options.chain_call_control.failed_number === 0 ){
+        mod_toastr.success( 'Selected files imported into the current folder' );
+        Galaxy.modal.hide();
+      } else {
+        mod_toastr.error( 'Something went wrong :(' );
+      }
+      return true;
+    }
+    var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + 
+                                                       '&source=userdir_file' +
+                                                       '&path=' + popped_item ) )
+    promise.done( function( response ){
+              that.updateProgress();
+              that.chainCallImportingUserdirFiles( paths );
+            } )
+            .fail( function(){
+              that.options.chain_call_control.failed_number += 1;
+              that.updateProgress();
+              that.chainCallImportingUserdirFiles( paths );
+            } );
+  },
+
+  /**
+   * Take the array of paths and createa request for each of them
+   * calling them in chain. Update the progress bar in between each.
+   * @param  {array} paths           paths relative to Galaxy root folder
+   * @param  {boolean} preserve_dirs indicates whether to preserve folder structure
+   * @param  {boolean} link_data     copy files to Galaxy or link instead
+   * @param  {str} source            string representing what type of folder 
+   *                                 is the source of import
+   */
+  chainCallImportingFolders: function(paths, preserve_dirs, link_data, source){
+    // need to check which paths to call
+    var that = this;
+    var popped_item = paths.pop();
+    if (typeof popped_item == "undefined") {
+      if (this.options.chain_call_control.failed_number === 0){
+        mod_toastr.success('Selected folders and their contents imported into the current folder');
+        Galaxy.modal.hide();
+      } else {
+        // TODO better error report
+        mod_toastr.error('Something went wrong :(');
+      }
+      return true;
+    }
+    var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
+                                                      '&source=' + source +
+                                                      '&path=' + popped_item +
+                                                      '&preserve_dirs=' + preserve_dirs +
+                                                      '&link_data=' + link_data))
+    promise.done(function(response){
+              that.updateProgress();
+              that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+            })
+            .fail(function(){
+              that.options.chain_call_control.failed_number += 1;
+              that.updateProgress();
+              that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+            });
+  },
+
+  /**
+   * Take the array of hdas and create a request for each. 
+   * Call them in chain and update progress bar in between each.
+   * @param  {array} hdas_set array of empty hda objects
+   */
+  chainCallAddingHdas: function( hdas_set ){
     var self = this;
     this.added_hdas = new mod_library_model.Folder();
     var popped_item = hdas_set.pop();
-    if (typeof popped_item === "undefined") {
-      if (this.options.chain_call_control.failed_number === 0){
-        mod_toastr.success('Selected datasets from history added to the folder');
-      } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
-        mod_toastr.error('There was an error and no datasets were added to the folder.');
-      } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
-        mod_toastr.warning('Some of the datasets could not be added to the folder');
+    if ( typeof popped_item == "undefined" ) {
+      if ( this.options.chain_call_control.failed_number === 0 ){
+        mod_toastr.success( 'Selected datasets from history added to the folder' );
+      } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
+        mod_toastr.error( 'There was an error and no datasets were added to the folder.' );
+      } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
+        mod_toastr.warning( 'Some of the datasets could not be added to the folder' );
       }
       Galaxy.modal.hide();
       return this.added_hdas;
     }
-    var promise = $.when(popped_item.save({from_hda_id: popped_item.get('from_hda_id')}));
+    var promise = $.when( popped_item.save( { from_hda_id: popped_item.get( 'from_hda_id' ) } ) );
 
-    promise.done(function(model){
-              // we are fine
-              Galaxy.libraries.folderListView.collection.add(model);
+    promise.done( function( model ){
+              Galaxy.libraries.folderListView.collection.add( model );
               self.updateProgress();
-              self.chainCallAddingHdas(hdas_set);
+              self.chainCallAddingHdas( hdas_set );
             })
-            .fail(function(){
-              // we have a problem
+            .fail( function(){
               self.options.chain_call_control.failed_number += 1;
               self.updateProgress();
-              self.chainCallAddingHdas(hdas_set);
+              self.chainCallAddingHdas( hdas_set );
             });
   },
 
   /**
+   * Take the array of lddas, create request for each and 
+   * call them in chain. Update progress bar in between each.
+   * @param  {array} lddas_set array of lddas to delete
+   */
+  chainCallDeletingHdas: function( lddas_set ){
+  var self = this;
+  this.deleted_lddas = new mod_library_model.Folder();
+  var popped_item = lddas_set.pop();
+  if ( typeof popped_item === "undefined" ) {
+    if ( this.options.chain_call_control.failed_number === 0 ){
+      mod_toastr.success( 'Selected datasets deleted' );
+    } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
+      mod_toastr.error( 'There was an error and no datasets were deleted.' );
+    } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
+      mod_toastr.warning( 'Some of the datasets could not be deleted' );
+    }
+    Galaxy.modal.hide();
+    return this.deleted_lddas;
+  }
+  var promise = $.when( popped_item.destroy() );
+
+  promise.done( function( dataset ){
+            Galaxy.libraries.folderListView.collection.remove( popped_item.id );
+            self.updateProgress();
+            // add the deleted dataset to collection, triggers rendering
+            if ( Galaxy.libraries.folderListView.options.include_deleted ){
+              var updated_dataset = new mod_library_model.Item( dataset );
+              Galaxy.libraries.folderListView.collection.add( updated_dataset );
+            }
+            self.chainCallDeletingHdas( lddas_set );
+          })
+          .fail( function(){
+            self.options.chain_call_control.failed_number += 1;
+            self.updateProgress();
+            self.chainCallDeletingHdas( lddas_set );
+          });
+  },
+
+  /**
    * Handles the click on 'show deleted' checkbox
    */
   checkIncludeDeleted: function(event){
@@ -764,43 +794,6 @@
     }
   },
 
-  chainCallDeletingHdas: function(lddas_set){
-  var self = this;
-  this.deleted_lddas = new mod_library_model.Folder();
-  var popped_item = lddas_set.pop();
-  if (typeof popped_item === "undefined") {
-    if (this.options.chain_call_control.failed_number === 0){
-      mod_toastr.success('Selected datasets deleted');
-    } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){
-      mod_toastr.error('There was an error and no datasets were deleted.');
-    } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){
-      mod_toastr.warning('Some of the datasets could not be deleted');
-    }
-    Galaxy.modal.hide();
-    return this.deleted_lddas;
-  }
-  var promise = $.when(popped_item.destroy());
-
-  promise.done(function(dataset){
-            // we are fine
-            Galaxy.libraries.folderListView.collection.remove(popped_item.id);
-            self.updateProgress();
-            // add the deleted dataset to collection, triggers rendering
-            if (Galaxy.libraries.folderListView.options.include_deleted){
-              var updated_dataset = new mod_library_model.Item(dataset);
-              Galaxy.libraries.folderListView.collection.add(updated_dataset);
-            }
-            // execute next request
-            self.chainCallDeletingHdas(lddas_set);
-          })
-          .fail(function(){
-            // we have a problem
-            self.options.chain_call_control.failed_number += 1;
-            self.updateProgress();
-            // execute next request
-            self.chainCallDeletingHdas(lddas_set);
-          });
-  },
 
   showLibInfo: function(){
     var library_id = Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;
@@ -988,7 +981,7 @@
     var tmpl_array = [];
 
     tmpl_array.push('<div class="import_text">');
-    tmpl_array.push('Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>');
+    tmpl_array.push('Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>');
     tmpl_array.push('</div>');
     tmpl_array.push('<div class="progress">');
     tmpl_array.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');

diff -r aec146e3828b16812ca24c5f8651ba3d0d483a6a -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 static/scripts/packed/libs/jquery/jstree.js
--- a/static/scripts/packed/libs/jquery/jstree.js
+++ b/static/scripts/packed/libs/jquery/jstree.js
@@ -1,4 +1,4 @@
-(function(a){if(typeof define==="function"&&define.amd){}else{if(typeof exports==="object"){a(require("jquery"))}else{a(jQuery)}}}(function(i,e){
+(function(a){if(typeof define==="function"&&define.amd){define(["jquery"],a)}else{if(typeof exports==="object"){a(require("jquery"))}else{a(jQuery)}}}(function(i,e){
 /*
  * jsTree 3.0.3
  * http://jstree.com/

diff -r aec146e3828b16812ca24c5f8651ba3d0d483a6a -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 static/scripts/packed/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","libs/jquery/jstree","mvc/library/library-model"],function(c,e,f,b,d){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}else{f.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var g=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new d.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";g.push(m)}this.options.chain_call_control.total_number=g.length;jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCall(g,n)},chainCall:function(h,k){var g=this;var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCall(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCall(h,k)})},initProgress:function(g){this.progress=0;this.progressStep=g},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon")}else{f.error("An error occurred :(")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred :(")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Enter paths relative to Galaxy root",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Select folders or files to import",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){$("#jstree_browser").jstree("destroy");var l=$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var l=this.modal.$el.find(".link-checkbox").is(":checked");var k=$("textarea#import_paths").val();if(!k){f.info("Please enter a path relative to Galaxy root")}else{this.modal.disableButton("Import");k=k.split("\n");var j=[];for(var h=k.length-1;h>=0;h--){trimmed=k[h].trim();if(trimmed.length!==0){j.push(trimmed)}}this.initChainCallControl(j.length);this.chainCallImportingFolders(j,g,l,"admin_path")}},initChainCallControl:function(g){var h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));this.progress=0;this.progressStep=100/g;this.options.chain_call_control.total_number=g;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(l){var h=$("#jstree_browser").jstree().get_selected(true);var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var n=[];if(h.length<1){f.info("You have to select some items first")}else{this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;for(var j=h.length-1;j>=0;j--){if(h[j].li_attr.full_path!==undefined){n.push(h[j].li_attr.full_path)}}var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/n.length;this.progress=0;this.options.chain_call_control.total_number=n.length;var k=h[0].type;if(k==="folder"){this.chainCallImportingFolders(n,g,o,"userdir_folder")}else{if(k==="file"){this.chainCallImportingUserdirFiles(n)}}}},chainCallImportingUserdirFiles:function(j){var g=this;var h=j.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}return true}var i=$.when($.post("/api/libraries/datasets?encoded_folder_id="+g.id+"&source=userdir_file&path="+h));i.done(function(k){g.updateProgress();g.chainCallImportingUserdirFiles(j)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingUserdirFiles(j)})},chainCallImportingFolders:function(l,g,m,j){var h=this;var i=l.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder");Galaxy.modal.hide()}else{f.error("Something went wrong :(")}return true}var k=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+j+"&path="+i+"&preserve_dirs="+g+"&link_data="+m));k.done(function(n){h.updateProgress();h.chainCallImportingFolders(l,g,m,j)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(l,g,m,j)})},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");if(l.length<1){f.info("You have to select some datasets first")}else{this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});var m=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(m({folder_name:this.options.folder_name}));this.progressStep=100/g.length;this.progress=0;var k=[];for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.options.chain_call_control.total_number=k.length;this.chainCallAddingHdas(k)}},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You have to select some datasets first")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push("   <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push('   <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li class="divider"></li>');tmpl_array.push('        <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push("<% } else { %>");tmpl_array.push('     <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push('       <span class="completion_span">0% Complete</span>');g.push("   </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div id="jstree_browser">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push('   <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history:  ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push("   <% _.each(histories, function(history) { %>");g.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push("   <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push('   <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){g.is_admin=Galaxy.currUser.isAdmin();g.is_anonym=Galaxy.currUser.isAnonymous();if(g.user_library_import_dir!==null||g.allow_library_path_paste!==false||g.library_import_dir!==null){g.mutiple_add_dataset_options=true}}this.$el.html(h(g))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(h){h.preventDefault();h.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(h){var g=h.templateBulkImportInModal();h.modal=Galaxy.modal;h.modal.show({closing_events:true,title:"Import into History",body:g({histories:h.histories.models}),buttons:{Import:function(){h.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var j=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=j;var g=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});var l=[];for(var h=g.length-1;h>=0;h--){var f=g[h];var k=new c.HistoryItem();k.url=k.urlRoot+j+"/contents";k.content=f;k.source="library";l.push(k)}this.initChainCallControl({length:l.length,action:"to_history",history_name:m});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+j);this.chainCallImportingIntoHistory(l,m)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}else{e.error("An error occurred :(")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesFromHistory();var h=f.options.full_path[f.options.full_path.length-1][1];f.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+h,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(i){f.fetchAndDisplayHistoryContents(i.target.value)})}else{e.error("An error ocurred :(")}})},importFilesFromPathModal:function(){var g=this;this.modal=Galaxy.modal;var f=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Enter paths relative to Galaxy root",body:f({}),buttons:{Import:function(){g.importFromPathsClicked(g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+g.id,{trigger:true})}})},importFilesFromUserdirModal:function(){var g=this;this.modal=Galaxy.modal;var f=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Select folders or files to import",body:f({}),buttons:{Import:function(){g.importFromUserdirClicked(g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+g.id,{trigger:true})}});this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(h){if(h.target.value==="jstree-disable-folders"){g.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(h.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(f){var h=this;this.options=_.extend(this.options,f);var g=this.options.disabled_jstree_element;this.jstree=new c.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+g;this.jstree.fetch({success:function(j,i){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(k){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:j},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importFromPathsClicked:function(){var f=this.modal.$el.find(".preserve-checkbox").is(":checked");var k=this.modal.$el.find(".link-checkbox").is(":checked");var j=$("textarea#import_paths").val();var h=[];if(!j){e.info("Please enter a path relative to Galaxy root")}else{this.modal.disableButton("Import");j=j.split("\n");for(var g=j.length-1;g>=0;g--){trimmed=j[g].trim();if(trimmed.length!==0){h.push(trimmed)}}this.initChainCallControl({length:h.length,action:"adding_datasets"});this.chainCallImportingFolders(h,f,k,"admin_path")}},initChainCallControl:function(f){var g;switch(f.action){case"adding_datasets":g=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(g({folder_name:this.options.folder_name}));break;case"deleting_datasets":g=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(g());break;case"to_history":g=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(g({history_name:f.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/f.length;this.options.chain_call_control.total_number=f.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(k){var g=$("#jstree_browser").jstree().get_selected(true);var f=this.modal.$el.find(".preserve-checkbox").is(":checked");var m=this.modal.$el.find(".link-checkbox").is(":checked");var j=g[0].type;var l=[];if(g.length<1){e.info("You have to select some items first")}else{this.modal.disableButton("Import");for(var h=g.length-1;h>=0;h--){if(g[h].li_attr.full_path!==undefined){l.push(g[h].li_attr.full_path)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders(l,f,m,"userdir_folder")}else{if(j==="file"){this.chainCallImportingUserdirFiles(l)}}}},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},addAllDatasetsFromHistory:function(){var k=this.modal.$el.find("#selected_history_content").find(":checked");var f=[];var j=[];if(k.length<1){e.info("You have to select some datasets first")}else{this.modal.disableButton("Add");k.each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.initChainCallControl({length:j.length,action:"adding_datasets"});this.chainCallAddingHdas(j)}},chainCallImportingIntoHistory:function(g,j){var f=this;var h=g.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCallImportingIntoHistory(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallImportingIntoHistory(g,j)})},chainCallImportingUserdirFiles:function(i){var f=this;var g=i.pop();if(typeof g==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{e.error("Something went wrong :(")}return true}var h=$.when($.post("/api/libraries/datasets?encoded_folder_id="+f.id+"&source=userdir_file&path="+g));h.done(function(j){f.updateProgress();f.chainCallImportingUserdirFiles(i)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallImportingUserdirFiles(i)})},chainCallImportingFolders:function(k,f,l,i){var g=this;var h=k.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected folders and their contents imported into the current folder");Galaxy.modal.hide()}else{e.error("Something went wrong :(")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+g.id+"&source="+i+"&path="+h+"&preserve_dirs="+f+"&link_data="+l));j.done(function(m){g.updateProgress();g.chainCallImportingFolders(k,f,l,i)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingFolders(k,f,l,i)})},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},showLibInfo:function(){var g=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var f=null;var h=this;if(Galaxy.libraries.libraryListView!==null){f=Galaxy.libraries.libraryListView.collection.get(g);this.showLibInfoModal(f)}else{f=new c.Library({id:g});f.fetch({success:function(){h.showLibInfoModal(f)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}},showLibInfoModal:function(f){var g=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:g({library:f}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(f){switch(f.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();e.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push("   <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push('   <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li class="divider"></li>');tmpl_array.push('        <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push("<% } else { %>");tmpl_array.push('     <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push("     </button>");tmpl_array.push('     <ul class="dropdown-menu" role="menu">');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push("     </ul>");tmpl_array.push("   </div>");tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push("   <% _.each(histories, function(history) { %>");f.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push("   <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push('       <span class="completion_span">0% Complete</span>');f.push("   </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push('       <span class="completion_span">0% Complete</span>');f.push("   </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push('       <span class="completion_span">0% Complete</span>');f.push("   </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateBrowserModal:function(){var f=[];f.push('<div id="file_browser_modal">');f.push('<div style="margin-bottom:1em;">');f.push('<label class="radio-inline">');f.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');f.push("</label>");f.push('<label class="radio-inline">');f.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');f.push("</label>");f.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');f.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');f.push("Preserve directory structure");f.push(" </label>");f.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');f.push('   <input class="link-checkbox" type="checkbox" value="link_files">');f.push("Link files instead of copying");f.push(" </label>");f.push("</div>");f.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');f.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');f.push('<div id="jstree_browser">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateImportPathModal:function(){var f=[];f.push('<div id="file_browser_modal">');f.push('<label class="checkbox-inline jstree-preserve-structure">');f.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');f.push("Preserve directory structure");f.push(" </label>");f.push('<label class="checkbox-inline jstree-link-files">');f.push('   <input class="link-checkbox" type="checkbox" value="link_files">');f.push("Link files instead of copying");f.push(" </label>");f.push("</div>");f.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');f.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');f.push("</div>");return _.template(f.join(""))},templateAddFilesFromHistory:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history:  ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push("   <% _.each(histories, function(history) { %>");f.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push("   <% }); %>");f.push("</select>");f.push("</div>");f.push("<br/>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("<strong>Choose the datasets to import:</strong>");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push('   <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file

diff -r aec146e3828b16812ca24c5f8651ba3d0d483a6a -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 templates/webapps/galaxy/galaxy.panels.mako
--- a/templates/webapps/galaxy/galaxy.panels.mako
+++ b/templates/webapps/galaxy/galaxy.panels.mako
@@ -32,7 +32,6 @@
         'libs/jquery/jquery',
         'libs/jquery/jquery-ui',
         "libs/jquery/select2",
-        "libs/jquery/jstree",
         'libs/bootstrap',
         'libs/underscore',
         'libs/backbone/backbone',


https://bitbucket.org/galaxy/galaxy-central/commits/c059c1061efa/
Changeset:   c059c1061efa
User:        martenson
Date:        2014-09-16 22:03:05+00:00
Summary:     Merge
Affected #:  7 files

diff -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 -r c059c1061efa625d6ad1ff2fc298db03b01e2c61 client/GruntFile.js
--- a/client/GruntFile.js
+++ b/client/GruntFile.js
@@ -2,8 +2,10 @@
 
   // Project configuration.
   grunt.initConfig({
-    pkg: grunt.file.readJSON('package.json'),
+    pkg: grunt.file.readJSON( 'package.json' ),
 
+    // default task
+    // use 'grunt copy' to copy the entire <galaxy>/client/galaxy/scripts dir into <galaxy>/static/scripts
     copy: {
       main: {
         expand: true,
@@ -11,11 +13,18 @@
         src: '**',
         dest: '../static/scripts/'
       }
+    },
+
+    // use 'grunt watch' (from a new tab in your terminal) to have grunt re-copy changed files automatically
+    watch: {
+        // watch for changes in the src dir
+        files: [ 'galaxy/scripts/**' ],
+        tasks: [ 'default' ]
     }
-
   });
 
-  grunt.loadNpmTasks('grunt-contrib-copy');
+  grunt.loadNpmTasks( 'grunt-contrib-watch' );
+  grunt.loadNpmTasks( 'grunt-contrib-copy');
 
-  grunt.registerTask('default', ['copy']);
+  grunt.registerTask( 'default', [ 'copy' ] );
 };

diff -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 -r c059c1061efa625d6ad1ff2fc298db03b01e2c61 client/package.json
--- a/client/package.json
+++ b/client/package.json
@@ -6,6 +6,8 @@
     "galaxy"
   ],
   "devDependencies": {
-    "grunt-contrib-copy": "^0.5.0"
+    "grunt": "^0.4.5",
+    "grunt-contrib-copy": "^0.5.0",
+    "grunt-contrib-watch": "^0.6.1"
   }
 }

diff -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 -r c059c1061efa625d6ad1ff2fc298db03b01e2c61 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -137,7 +137,6 @@
         self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ]
         self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
         self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root )
-        self.dependency_resolvers_config_file = resolve_path( kwargs.get( 'dependency_resolvers_config_file', 'dependency_resolvers_conf.xml' ), self.root )
         self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) )
         self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) )
         self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") )
@@ -384,6 +383,7 @@
             external_service_type_config_file = [ 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample', 'config/external_service_types_conf.xml.sample' ],
             job_config_file = [ 'job_conf.xml', 'config/job_conf.xml' ],
             job_metrics_config_file = [ 'job_metrics_conf.xml', 'config/job_metrics_conf.xml' ],
+            dependency_resolvers_config_file = [ 'dependency_resolvers_conf.xml', 'config/dependency_resolvers_conf.xml' ],
             job_resource_params_file = [ 'job_resource_params_conf.xml', 'config/job_resource_params_conf.xml' ],
             migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ],
             object_store_config_file = [ 'object_store_conf.xml', 'config/object_store_conf.xml' ],

diff -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 -r c059c1061efa625d6ad1ff2fc298db03b01e2c61 static/scripts/mvc/ui/ui-checkbox.js
--- /dev/null
+++ b/static/scripts/mvc/ui/ui-checkbox.js
@@ -0,0 +1,91 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// plugin
+var View = Backbone.View.extend({
+    // options
+    optionsDefault: {
+        value           : '',
+        visible         : true,
+        cls             : '',
+        data            : [],
+        id              : Utils.uuid()
+    },
+    
+    // initialize
+    initialize : function(options) {
+        // configure options
+        this.options = Utils.merge(options, this.optionsDefault);
+            
+        // create new element
+        this.setElement(this._template(this.options));
+        
+        // hide input field
+        if (!this.options.visible) {
+            this.$el.hide();
+        }
+        
+        // set initial value
+        if (this.options.value) {
+            this.value(this.options.value);
+        }
+        
+        // current value
+        this.current = this.options.value;
+        
+        // onchange event handler. fires on user activity.
+        var self = this;
+        this.$el.find('input').on('change', function() {        
+            self.value(self._getValue());
+        });
+    },
+    
+    // value
+    value : function (new_val) {
+        // get current value
+        var before = this.current;
+        
+        // set new value
+        if (new_val !== undefined) {
+            this.$el.find('label').removeClass('active');
+            this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
+            this.current = new_val;
+        }
+
+        // check value
+        var after = this.current;
+        if (after != before && this.options.onchange) {
+            this.options.onchange(this.current);
+        }
+
+        // get and return value
+        return this.current;
+    },
+    
+    // get value
+    _getValue: function() {
+        var selected = this.$el.find(':checked');
+        var value = null;
+        if (selected.length > 0) {
+            value = selected.val();
+        }
+        return value;
+    },
+    
+    // element
+    _template: function(options) {
+        var tmpl =  '<div class="ui-checkbox">';
+        for (key in options.data) {
+            var pair = options.data[key];
+            tmpl +=     '<input type="checkbox" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + '<br>';
+        }
+        tmpl +=     '</div>';
+        return tmpl;
+    }
+});
+
+return {
+    View : View
+};
+
+});

diff -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 -r c059c1061efa625d6ad1ff2fc298db03b01e2c61 static/scripts/mvc/ui/ui-radiobutton.js
--- /dev/null
+++ b/static/scripts/mvc/ui/ui-radiobutton.js
@@ -0,0 +1,93 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// plugin
+var View = Backbone.View.extend({
+    // options
+    optionsDefault: {
+        value           : '',
+        visible         : true,
+        cls             : '',
+        data            : [],
+        id              : Utils.uuid()
+    },
+    
+    // initialize
+    initialize : function(options) {
+        // configure options
+        this.options = Utils.merge(options, this.optionsDefault);
+            
+        // create new element
+        this.setElement(this._template(this.options));
+        
+        // hide input field
+        if (!this.options.visible) {
+            this.$el.hide();
+        }
+        
+        // set initial value
+        if (this.options.value) {
+            this.value(this.options.value);
+        }
+        
+        // current value
+        this.current = this.options.value;
+        
+        // onchange event handler. fires on user activity.
+        var self = this;
+        this.$el.find('input').on('change', function() {        
+            self.value(self._getValue());
+        });
+    },
+    
+    // value
+    value : function (new_val) {
+        // get current value
+        var before = this.current;
+        
+        // set new value
+        if (new_val !== undefined) {
+            this.$el.find('label').removeClass('active');
+            this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
+            this.current = new_val;
+        }
+
+        // check value
+        var after = this.current;
+        if (after != before && this.options.onchange) {
+            this.options.onchange(this.current);
+        }
+
+        // get and return value
+        return this.current;
+    },
+    
+    // get value
+    _getValue: function() {
+        var selected = this.$el.find(':checked');
+        var value = null;
+        if (selected.length > 0) {
+            value = selected.val();
+        }
+        return value;
+    },
+    
+    // element
+    _template: function(options) {
+        var tmpl =  '<div class="btn-group ui-radiobutton" data-toggle="buttons">';
+        for (key in options.data) {
+            var pair = options.data[key];
+            tmpl +=     '<label class="btn btn-default">' +
+                            '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label +
+                        '</label>';
+        }
+        tmpl +=     '</div>';
+        return tmpl;
+    }
+});
+
+return {
+    View : View
+};
+
+});

diff -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 -r c059c1061efa625d6ad1ff2fc298db03b01e2c61 static/scripts/packed/mvc/ui/ui-checkbox.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui/ui-checkbox.js
@@ -0,0 +1,1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="ui-checkbox">';for(key in d.data){var e=d.data[key];c+='<input type="checkbox" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"<br>"}c+="</div>";return c}});return{View:b}});
\ No newline at end of file

diff -r f163dd7c2ccdd908b4f1f4e30defbbd20ee0da58 -r c059c1061efa625d6ad1ff2fc298db03b01e2c61 static/scripts/packed/mvc/ui/ui-radiobutton.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui/ui-radiobutton.js
@@ -0,0 +1,1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in d.data){var e=d.data[key];c+='<label class="btn btn-default"><input type="radio" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"</label>"}c+="</div>";return c}});return{View:b}});
\ No newline at end of file


https://bitbucket.org/galaxy/galaxy-central/commits/7ddb0d7b4b12/
Changeset:   7ddb0d7b4b12
User:        jmchilton
Date:        2014-09-17 01:40:35+00:00
Summary:     Merged in martenson/galaxy-central-marten (pull request #497)

importing into library folders from Galaxy filesystem
Affected #:  37 files

diff -r 38be704a932fafd27b01034ae9daf83a465062bf -r 7ddb0d7b4b128089322b441c77eceaea5d993312 client/galaxy/scripts/galaxy.library.js
--- a/client/galaxy/scripts/galaxy.library.js
+++ b/client/galaxy/scripts/galaxy.library.js
@@ -47,7 +47,8 @@
     "folders/:folder_id/datasets/:dataset_id"                       : "dataset_detail",
     "folders/:folder_id/datasets/:dataset_id/permissions"           : "dataset_permissions",
     "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id"     : "dataset_version",
-    "folders/:folder_id/download/:format"                           : "download"
+    "folders/:folder_id/download/:format"                           : "download",
+    "folders/:folder_id/import/:source"                             : "import_datasets"
   },
 
   back: function() {
@@ -147,6 +148,15 @@
           }
           Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
        });
+       this.library_router.on('route:import_datasets', function(folder_id, source){
+          if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){
+            Galaxy.libraries.folderToolbarView.showImportModal({source:source});
+          } else {
+            Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id});
+            Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id});
+            Galaxy.libraries.folderToolbarView.showImportModal({source: source});
+          }
+       });
 
     Backbone.history.start({pushState: false});
     }

This diff is so big that we needed to truncate the remainder.

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 11 new changesets

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