From 4064d0c5980644f29ac06b83f28e7064479f28db Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <crusoe@ucdavis.edu>
Date: Fri, 11 Sep 2015 15:08:44 -0700
Subject: [PATCH] add Oxli datatypes

---
 config/datatypes_conf.xml.sample | 12 +++++
 lib/galaxy/datatypes/binary.py   | 80 ++++++++++++++++++++++++++++++++
 2 files changed, 92 insertions(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index dbfcf3fc3cf..59d04ad8bdb 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -412,6 +412,12 @@
     <datatype extension="xmfa" type="galaxy.datatypes.msa:MauveXmfa" display_in_upload="True" />
 
     <datatype extension="RData" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
+    <datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="oxlits" type="galaxy.datatypes.binary:OxliTagSet" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="oxlist" type="galaxy.datatypes.binary:OxliStopTags" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="oxliss" type="galaxy.datatypes.binary:OxliSubset" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="oxlils" type="galaxy.datatypes.binary:OxliLabelSet" mimetype="application/octet-stream" display_in_upload="true"/>
   </registration>
   <sniffers>
     <!--
@@ -500,6 +506,12 @@
     module is fixed to not read the entire file.
     <sniffer type="galaxy.datatypes.assembly:Amos"/>
     -->
+    <sniffer type="galaxy.datatypes.binary:OxliCountGraph"/>
+    <sniffer type="galaxy.datatypes.binary:OxliNodeGraph"/>
+    <sniffer type="galaxy.datatypes.binary:OxliTagSet"/>
+    <sniffer type="galaxy.datatypes.binary:OxliStopTags"/>
+    <sniffer type="galaxy.datatypes.binary:OxliSubset"/>
+    <sniffer type="galaxy.datatypes.binary:OxliLabelSet"/>
   </sniffers>
   <build_sites>
       <!--
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 337b4aae139..67599f8ba8e 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -908,3 +908,83 @@ class RData( Binary ):
             return False
 
 Binary.register_sniffable_binary_format('RData', 'RData', RData)
+
+
+class OxliBinary(Binary):
+
+    def __init__(self, **kwd):
+        Binary.__init__(self, **kwd)
+
+    def sniff(self, filename, filetype):
+        try:
+            with open(filename) as fileobj:
+                header = fileobj.read(4)
+                if binascii.b2a_hex(header) == binascii.hexlify('OXLI'):
+                    fileobj.seek(1)
+                    ftype = fileobj.read(1)
+                    if binascii.b2a_hex(ftype) == filetype:
+                        return True
+            return False
+        except IOError:
+            return False
+
+
+class OxliCountGraph(OxliBinary):
+
+    def __init__(self, **kwd):
+        OxliBinary.__init__(self, **kwd)
+
+    def sniff(self, filename):
+        return OxliBinary.sniff(self, filename, "01")
+
+
+class OxliNodeGraph(OxliBinary):
+
+    def __init__(self, **kwd):
+        OxliBinary.__init__(self, **kwd)
+
+    def sniff(self, filename):
+        return OxliBinary.sniff(self, filename, "02")
+
+
+class OxliTagSet(OxliBinary):
+
+    def __init__(self, **kwd):
+        OxliBinary.__init__(self, **kwd)
+
+    def sniff(self, filename):
+        return OxliBinary.sniff(self, filename, "03")
+
+
+class OxliStopTags(OxliBinary):
+
+    def __init__(self, **kwd):
+        OxliBinary.__init__(self, **kwd)
+
+    def sniff(self, filename):
+        return OxliBinary.sniff(self, filename, "04")
+
+
+class OxliSubset(OxliBinary):
+
+    def __init__(self, **kwd):
+        OxliBinary.__init__(self, **kwd)
+
+    def sniff(self, filename):
+        return OxliBinary.sniff(self, filename, "05")
+
+
+class OxliLabelSet(OxliBinary):
+
+    def __init__(self, **kwd):
+        OxliBinary.__init__(self, **kwd)
+
+    def sniff(self, filename):
+        return OxliBinary.sniff(self, filename, "06")
+
+Binary.register_sniffable_binary_format("oxli.countgraph", "oxlicg", OxliCountGraph)
+Binary.register_sniffable_binary_format("oxli.nodegraph", "oxling", OxliNodeGraph)
+Binary.register_sniffable_binary_format("oxli.tagset", "oxlits", OxliTagSet)
+Binary.register_sniffable_binary_format("oxli.stoptags", "oxlist", OxliStopTags)
+Binary.register_sniffable_binary_format("oxli.subset", "oxliss", OxliSubset)
+Binary.register_sniffable_binary_format("oxli.labelset", "oxlils", OxliLabelSet)