Mercurial > repos > yating-l > hubarchivecreator

--- a/trackHub/README.md	Wed Dec 28 17:56:36 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-This folder exists to configure Galaxy to handle the files generated by HubArchiveCreator tool
-
-* The **content** of datatypes_conf.xml should go inside config/datatypes_conf.xml, under \<registration\> (Copy config/datatypes_conf.xml.sample to config/datatypes_conf.xml if it does not exist yet)
-* The content of tracks_partial.py should go inside `lib/galaxy/datatypes/tracks.py`
-* trackhub.xml should go inside display_application/ucsc/
-
-
-TODO:
-
-- [x] Create a script to copy all these files directly into galaxy => Done but not usable now I have changed the datatype to match Galaxy IUC
-- [ ] Need to modify the script `util/add_datatype.py` to match the changes introduced in https://github.com/galaxyproject/galaxy/pull/2348
-- [x] Create a package in ToolShed that install directly this when installing HubArchiveCreator => Not recommended by Galaxy IUC and team
--- a/trackHub/datatypes_conf.xml	Wed Dec 28 17:56:36 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-<datatype extension="trackhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
-    <display file="ucsc/trackhub.xml" />
-</datatype>
--- a/trackHub/trackhub.xml	Wed Dec 28 17:56:36 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<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>
--- a/trackHub/tracks_partial.py	Wed Dec 28 17:56:36 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-"""
-HubAssembly datatype
-"""
-import logging
-
-from galaxy.datatypes.text import Html
-
-log = logging.getLogger( __name__ )
-
-# !!! README !!! The content of this file should be added in tracks.py, but do it carefully!
-# Don't erase the existing content
-
-
-class UCSCTrackHub( Html ):
-    """
-    derived class for BioC data structures in Galaxy
-    """
-
-    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)]
-
-        def create_tree(path, tree):
-            if path[0] in tree:
-                create_tree(path[1:], tree[path[0]])
-            else:
-                tree[path[0]] = {}
-                if len(path) == 1:
-                    return
-                else:
-                    create_tree(path[1:], tree[path[0]])
-
-        def print_tree(tree, level):
-            if len(tree) == 0:
-                return
-
-            for vertex in tree:
-                    composite_name = vertex
-                    bullet_point = '<li><a href="{0}>{0}</a></li>'.format(composite_name)
-                    rval.append(bullet_point)
-                    # Parent, so need to create a sub <ul>
-                    if len(tree[vertex]) > 0:
-                        rval.append('<ul>')
-                        print_tree(tree[vertex], level+1)
-                        rval.append('</ul>')
-
-        walkable_tree = {}
-
-        for composite_name_full_path, composite_file in self.get_composite_files(dataset=dataset).iteritems():
-            paths = composite_name_full_path.split('/')
-            # Prepare the tree from to perform a Depth First Search
-            create_tree(paths, walkable_tree)
-
-        # Perform a Depth First Search to print all the directory and files properly
-        print_tree(walkable_tree, 0)
-
-        # 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