From 0a9d038a5d75560bc27e1f20d833e435b2f90e6e Mon Sep 17 00:00:00 2001
From: remiarenco <remimarenco@gmail.com>
Date: Wed, 11 May 2016 21:48:25 -0400
Subject: [PATCH 1/8] Add the  composite datatype

---
 config/datatypes_conf.xml.sample    |  3 ++
 display_applications/ucsc/huba.xml  |  6 +++
 lib/galaxy/datatypes/hubAssembly.py | 58 +++++++++++++++++++++++++++++
 3 files changed, 67 insertions(+)
 create mode 100755 display_applications/ucsc/huba.xml
 create mode 100755 lib/galaxy/datatypes/hubAssembly.py

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 8e6426c851e..6801f10dc7f 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -530,6 +530,9 @@
     <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="huba" type="galaxy.datatypes.hubAssembly:HubAssembly" display_in_upload="true">
+    <display file="ucsc/huba.xml" />
+    </datatype>
   </registration>
   <sniffers>
     <!--
diff --git a/display_applications/ucsc/huba.xml b/display_applications/ucsc/huba.xml
new file mode 100755
index 00000000000..ae050797be7
--- /dev/null
+++ b/display_applications/ucsc/huba.xml
@@ -0,0 +1,6 @@
+<display id="ucsc_huba" 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" strip_https="True"/>
+    </link>
+</display>
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/hubAssembly.py b/lib/galaxy/datatypes/hubAssembly.py
new file mode 100755
index 00000000000..ea8085c1f90
--- /dev/null
+++ b/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
\ No newline at end of file

From 4002e4ed1dbf6bbdad89e2e2420295e37c6789f0 Mon Sep 17 00:00:00 2001
From: remiarenco <remimarenco@gmail.com>
Date: Wed, 11 May 2016 23:55:20 -0400
Subject: [PATCH 2/8] Pass pylint and better xml formatting

---
 config/datatypes_conf.xml.sample    | 2 +-
 lib/galaxy/datatypes/hubAssembly.py | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 6801f10dc7f..fb4edcab9ea 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -531,7 +531,7 @@
     <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="huba" type="galaxy.datatypes.hubAssembly:HubAssembly" display_in_upload="true">
-    <display file="ucsc/huba.xml" />
+        <display file="ucsc/huba.xml" />
     </datatype>
   </registration>
   <sniffers>
diff --git a/lib/galaxy/datatypes/hubAssembly.py b/lib/galaxy/datatypes/hubAssembly.py
index ea8085c1f90..357083b854e 100755
--- a/lib/galaxy/datatypes/hubAssembly.py
+++ b/lib/galaxy/datatypes/hubAssembly.py
@@ -55,4 +55,5 @@ class HubAssembly( Html ):
             return "Track Hub structure: Visualization in UCSC Track Hub"
 
     def sniff( self, filename ):
-        return False
\ No newline at end of file
+        return False
+

From e0ffb2d8d021248019c3a9a9d9e18ca0cdd9cf26 Mon Sep 17 00:00:00 2001
From: remiarenco <remimarenco@gmail.com>
Date: Fri, 13 May 2016 23:18:32 -0400
Subject: [PATCH 3/8] Following advices: renamed the extension to 'trackhub',
 renamed the huba.xml to trackhub.xml, changed iteritems to items, removed
 hubAssembly.py to port it into tracks.py

---
 config/datatypes_conf.xml.sample              |  4 +-
 .../ucsc/{huba.xml => trackhub.xml}           |  4 +-
 lib/galaxy/datatypes/tracks.py                | 55 +++++++++++++++++++
 3 files changed, 59 insertions(+), 4 deletions(-)
 rename display_applications/ucsc/{huba.xml => trackhub.xml} (80%)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index fb4edcab9ea..19d49f48399 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -530,8 +530,8 @@
     <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="huba" type="galaxy.datatypes.hubAssembly:HubAssembly" display_in_upload="true">
-        <display file="ucsc/huba.xml" />
+    <datatype extension="trakhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
+        <display file="ucsc/trackhub.xml" />
     </datatype>
   </registration>
   <sniffers>
diff --git a/display_applications/ucsc/huba.xml b/display_applications/ucsc/trackhub.xml
similarity index 80%
rename from display_applications/ucsc/huba.xml
rename to display_applications/ucsc/trackhub.xml
index ae050797be7..f87da3067bc 100755
--- a/display_applications/ucsc/huba.xml
+++ b/display_applications/ucsc/trackhub.xml
@@ -1,6 +1,6 @@
-<display id="ucsc_huba" version="1.0.0" name="display at Track Hub UCSC">
+<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" strip_https="True"/>
     </link>
-</display>
\ No newline at end of file
+</display>
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index 1e3bf09c57e..254dc9ff664 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -5,6 +5,15 @@ Datatype classes for tracks/track views within galaxy.
 import binary
 import logging
 
+# For UCSCTrackHub
+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__)
 
 # GeneTrack is no longer supported but leaving the datatype since
@@ -36,3 +45,49 @@ 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
+

From 873a5d9f725cf574550b88805c543ebb33ee3ffc Mon Sep 17 00:00:00 2001
From: remiarenco <remimarenco@gmail.com>
Date: Sat, 14 May 2016 08:32:41 -0400
Subject: [PATCH 4/8] Fix the uppercase in the extension (did not seem to
 affect the loading of the datatype/its use in Galaxy

---
 lib/galaxy/datatypes/tracks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index 254dc9ff664..e77bcc2dfe1 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -52,7 +52,7 @@ class UCSCTrackHub( Html ):
     Datatype for UCSC TrackHub
     """
 
-    file_ext = 'trackHub'
+    file_ext = 'trackhub'
     composite_type = 'auto_primary_file'
 
     def __init__(self, **kwd):

From 1f6d3bc47069b054c86687bf00a8cad2afdd43bd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Marenco?= <remi.marenco@gmail.com>
Date: Tue, 17 May 2016 20:07:31 -0400
Subject: [PATCH 5/8] Update datatypes_conf.xml.sample

Typo in the extension
---
 config/datatypes_conf.xml.sample | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 19d49f48399..241b22a6fc8 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -530,7 +530,7 @@
     <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="trakhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
+    <datatype extension="trackhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
         <display file="ucsc/trackhub.xml" />
     </datatype>
   </registration>

From 7cf435438817672854d524f8359c92675c36b046 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 18 May 2016 13:47:01 -0400
Subject: [PATCH 6/8] Remove blank lines in file.

---
 lib/galaxy/datatypes/hubAssembly.py | 1 -
 lib/galaxy/datatypes/tracks.py      | 1 -
 2 files changed, 2 deletions(-)

diff --git a/lib/galaxy/datatypes/hubAssembly.py b/lib/galaxy/datatypes/hubAssembly.py
index 357083b854e..06025ac3016 100755
--- a/lib/galaxy/datatypes/hubAssembly.py
+++ b/lib/galaxy/datatypes/hubAssembly.py
@@ -56,4 +56,3 @@ class HubAssembly( Html ):
 
     def sniff( self, filename ):
         return False
-
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index e77bcc2dfe1..a4f9594ee2f 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -90,4 +90,3 @@ class UCSCTrackHub( Html ):
 
     def sniff( self, filename ):
         return False
-

From e66cf8358940e9bf298de4e3416b952d44987c65 Mon Sep 17 00:00:00 2001
From: remimarenco <remi.marenco@gmail.com>
Date: Fri, 3 Jun 2016 11:51:57 -0400
Subject: [PATCH 7/8] Remove the support of Galaxy version <= 16.01

---
 lib/galaxy/datatypes/tracks.py | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index a4f9594ee2f..0d93c1a9bd3 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -5,14 +5,7 @@ Datatype classes for tracks/track views within galaxy.
 import binary
 import logging
 
-# For UCSCTrackHub
-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
+from galaxy.datatypes.text import Html
 
 log = logging.getLogger(__name__)
 

From 611ade3552d2cfe665156a64214e7a1e58d14683 Mon Sep 17 00:00:00 2001
From: remimarenco <remi.marenco@gmail.com>
Date: Fri, 3 Jun 2016 19:59:26 -0400
Subject: [PATCH 8/8] Remove the strip_https attribute because we don't need it
 anymore

---
 display_applications/ucsc/trackhub.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/display_applications/ucsc/trackhub.xml b/display_applications/ucsc/trackhub.xml
index f87da3067bc..45c34a07d03 100755
--- a/display_applications/ucsc/trackhub.xml
+++ b/display_applications/ucsc/trackhub.xml
@@ -1,6 +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_${DATASET_HASH}" allow_extra_files_access="True" strip_https="True"/>
+        <param type="data" name="hub_file" url="galaxy_${DATASET_HASH}" allow_extra_files_access="True" />
     </link>
 </display>