Merge pull request #2348 from remimarenco/huba_datatype

Add the trackhub composite datatype

config/datatypes_conf.xml.sample

@@ -533,6 +533,9 @@
     <datatype extension="mothur.axes" type="galaxy.datatypes.mothur:Axes" display_in_upload="true"/>
     <datatype extension="mothur.sff.flow" type="galaxy.datatypes.mothur:SffFlow" display_in_upload="true"/>
     <datatype extension="mothur.count_table" type="galaxy.datatypes.mothur:CountTable" display_in_upload="true"/>
+    <datatype extension="trackhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
+        <display file="ucsc/trackhub.xml" />
+    </datatype>
   </registration>
   <sniffers>
     <!--

display_applications/ucsc/trackhub.xml

@@ -0,0 +1,6 @@
+<display id="ucsc_trackhub" version="1.0.0" name="display at Track Hub UCSC">
+    <link id="main" name="main">
+        <url>https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=${qp($hub_file.url + '/myHub/hub.txt')}&amp;hgHub_do_firstDb=on&amp;hgHub_do_redirect=on&amp;hgHubConnect.remakeTrackHub=on</url>
+        <param type="data" name="hub_file" url="galaxy_${DATASET_HASH}" allow_extra_files_access="True" />
+    </link>
+</display>

lib/galaxy/datatypes/hubAssembly.py

@@ -0,0 +1,58 @@
+"""
+HubAssembly datatype
+"""
+import logging
+import galaxy.version as version
+
+# Support for Galaxy <= 16.01
+if version.VERSION_MAJOR <= "16.01":
+    from galaxy.datatypes.images import Html
+else:
+    from galaxy.datatypes.text import Html
+
+log = logging.getLogger(__name__)
+
+
+class HubAssembly( Html ):
+    """
+    derived class for BioC data structures in Galaxy
+    """
+
+    file_ext = 'huba'
+    composite_type = 'auto_primary_file'
+
+    def __init__(self, **kwd):
+        Html.__init__(self, **kwd)
+
+    def generate_primary_file( self, dataset=None ):
+        """
+        This is called only at upload to write the html file
+        cannot rename the datasets here - they come with the default unfortunately
+        """
+        rval = [
+            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            This composite dataset is composed of the following files:<p/><ul>' % (
+                self.file_ext)]
+        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
+            opt_text = ''
+            if composite_file.optional:
+                opt_text = ' (optional)'
+            rval.append('<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text) )
+        rval.append('</ul></html>')
+        return "\n".join(rval)
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Track Hub structure: Visualization in UCSC Track Hub"
+
+    def sniff( self, filename ):
+        return False

lib/galaxy/datatypes/tracks.py

@@ -5,6 +5,8 @@ Datatype classes for tracks/track views within galaxy.
 import binary
 import logging
 
+from galaxy.datatypes.text import Html
+
 log = logging.getLogger(__name__)
 
 # GeneTrack is no longer supported but leaving the datatype since
@@ -37,3 +39,48 @@ class GeneTrack( binary.Binary ):
     #                 link = "%s?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, galaxy_url )
     #                 ret_val.append( ( name, link ) )
     #         return ret_val
+
+
+class UCSCTrackHub( Html ):
+    """
+    Datatype for UCSC TrackHub
+    """
+
+    file_ext = 'trackhub'
+    composite_type = 'auto_primary_file'
+
+    def __init__(self, **kwd):
+        Html.__init__(self, **kwd)
+
+    def generate_primary_file( self, dataset=None ):
+        """
+        This is called only at upload to write the html file
+        cannot rename the datasets here - they come with the default unfortunately
+        """
+        rval = [
+            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            This composite dataset is composed of the following files:<p/><ul>' % (
+                self.file_ext)]
+        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).items():
+            opt_text = ''
+            if composite_file.optional:
+                opt_text = ' (optional)'
+            rval.append('<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text) )
+        rval.append('</ul></html>')
+        return "\n".join(rval)
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Track Hub structure: Visualization in UCSC Track Hub"
+
+    def sniff( self, filename ):
+        return False