Merge.

client/galaxy/scripts/viz/trackster.js

@@ -12,7 +12,6 @@ require(
 [
     // load js libraries
     'utils/utils',
-    'mvc/ui/icon-button',
     'libs/jquery/jquery.event.drag',
     'libs/jquery/jquery.event.hover',
     'libs/jquery/jquery.mousewheel',
@@ -32,9 +31,8 @@ require(
 });
 
 // trackster viewer
-define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization"], 
-        function(_, base, tracks, visualization) {
-
+define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ],
+        function(_, base, tracks, visualization, mod_icon_btn) {
 /**
  * User interface controls for trackster 
  */

config/datatypes_conf.xml.sample

@@ -140,6 +140,7 @@
     <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
     <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
     <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
+    <datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="True"/>
     <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
     <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
     <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
@@ -304,6 +305,7 @@
     <sniffer type="galaxy.datatypes.text:Arff"/>
     <sniffer type="galaxy.datatypes.text:Ipynb"/>
     <sniffer type="galaxy.datatypes.text:Json"/>
+    <sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/>
     <sniffer type="galaxy.datatypes.images:Jpg"/>
     <sniffer type="galaxy.datatypes.images:Png"/>
     <sniffer type="galaxy.datatypes.images:Tiff"/>

eggs.ini

@@ -15,7 +15,7 @@ no_auto = pbs_python
 bx_python = 0.7.2
 Cheetah = 2.2.2
 MarkupSafe = 0.12
-mercurial = 2.2.3
+mercurial = 3.2.4
 MySQL_python = 1.2.3c1
 PyRods = 3.2.4
 numpy = 1.6.0

lib/galaxy/datatypes/sequence.py

@@ -17,7 +17,7 @@ from galaxy.datatypes import metadata
 from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.sniff import get_test_fname, get_headers
 from galaxy.datatypes.metadata import MetadataElement
-
+from galaxy.datatypes.util.image_util import check_image_type
 
 try:
     eggs.require( "bx-python" )
@@ -814,3 +814,34 @@ class Lav( data.Text ):
         except:
             return False
 
+
+class RNADotPlotMatrix( data.Data ):
+    file_ext = "rna_eps"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = 'RNA Dot Plot format (Postscript derivative)'
+            dataset.blurb = data.nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff(self, filename):
+        """Determine if the file is in RNA dot plot format."""
+        if check_image_type( filename, ['EPS'] ):
+            seq = False
+            coor = False
+            pairs = False
+            with open( filename ) as handle:
+                for line in handle:
+                    line = line.strip()
+                    if line:
+                        if line.startswith('/sequence'):
+                            seq = True
+                        elif line.startswith('/coor'):
+                            coor = True
+                        elif line.startswith('/pairs'):
+                            pairs = True
+                    if seq and coor and pairs:
+                        return True
+        return False

lib/galaxy/datatypes/util/image_util.py

@@ -71,6 +71,4 @@ def get_image_ext ( file_path, image ):
         return 'pbm'
     if format == 'PGM':
         return 'pgm'
-    if format == 'EPS':
-        return 'eps'
     return None

lib/galaxy/tools/toolbox/base.py

@@ -394,7 +394,7 @@ class AbstractToolBox( object, Dictifiable ):
                         section.elems.stub_label( section_id )
                 self._integrated_tool_panel.append_section( key, section )
             elif elem.tag == 'label':
-                section.stub_label( key )
+                self._integrated_tool_panel.stub_label( key )
 
     def _write_integrated_tool_panel_config_file( self ):
         """

lib/tool_shed/util/hg_util.py

@@ -16,7 +16,7 @@ from mercurial import cmdutil
 from mercurial import commands
 from mercurial import hg
 from mercurial import ui
-from mercurial.changegroup import readbundle
+from mercurial.exchange import readbundle
 from mercurial.changegroup import readexactly
 
 from tool_shed.util import basic_util
@@ -26,7 +26,7 @@ log = logging.getLogger( __name__ )
 INITIAL_CHANGELOG_HASH = '000000000000'
 
 def add_changeset( repo_ui, repo, path_to_filename_in_archive ):
-    commands.add( repo_ui, repo, path_to_filename_in_archive )
+    commands.add( repo_ui, repo, str( path_to_filename_in_archive ) )
 
 def archive_repository_revision( app, repository, archive_dir, changeset_revision ):
     '''Create an un-versioned archive of a repository.'''
@@ -49,7 +49,7 @@ def bundle_to_json( fh ):
     command line) to a json object.
     """
     # See http://www.wstein.org/home/wstein/www/home/was/patches/hg_json
-    hg_unbundle10_obj = readbundle( fh, None )
+    hg_unbundle10_obj = readbundle( None, fh, None )
     groups = [ group for group in unpack_groups( hg_unbundle10_obj ) ]
     return json.dumps( groups, indent=4 )
 

static/scripts/viz/trackster.js

@@ -12,7 +12,6 @@ require(
 [
     // load js libraries
     'utils/utils',
-    'mvc/ui/icon-button',
     'libs/jquery/jquery.event.drag',
     'libs/jquery/jquery.event.hover',
     'libs/jquery/jquery.mousewheel',
@@ -32,9 +31,8 @@ require(
 });
 
 // trackster viewer
-define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization"], 
-        function(_, base, tracks, visualization) {
-
+define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ],
+        function(_, base, tracks, visualization, mod_icon_btn) {
 /**
  * User interface controls for trackster 
  */

templates/tagging_common.mako

@@ -89,7 +89,7 @@
 <%def name="render_tool_tagging_elements()">
     <%
         elt_id = int ( floor ( random()*maxint ) )
-        tags = trans.app.tag_handler.get_tool_tags( trans )
+        tags = trans.app.tag_handler.get_tool_tags()
     %>
     ${self.render_tagging_element_html(elt_id=elt_id, \
                                         tags=tags, \
@@ -105,7 +105,7 @@
     ## Build HTML.
     <% 
         elt_id = int ( floor ( random()*maxint ) ) 
-        community_tags = trans.app.tag_handler.get_community_tags( trans, item=tagged_item, limit=5 )
+        community_tags = trans.app.tag_handler.get_community_tags( item=tagged_item, limit=5 )
     %>
     ${self.render_tagging_element_html(elt_id=elt_id, \
                                         tags=community_tags, \