From f57076633a961f88de84156eb4f14e37d3b8cf62 Mon Sep 17 00:00:00 2001
From: Lee Kamentsky <leek@broadinstitute.org>
Date: Tue, 13 Oct 2015 09:21:34 -0400
Subject: [PATCH] Fixes #37 + test - the default xml was misformatted

---
 bioformats/omexml.py            | 16 ++++++++++------
 bioformats/tests/test_omexml.py | 18 ++++++++++++++++++
 2 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/bioformats/omexml.py b/bioformats/omexml.py
index 2bd5171..10a31d2 100644
--- a/bioformats/omexml.py
+++ b/bioformats/omexml.py
@@ -32,11 +32,11 @@ def xsd_now():
 NS_RE = r"http://www.openmicroscopy.org/Schemas/(?P<ns_key>.*)/[0-9/-]"
 
 default_xml = """<?xml version="1.0" encoding="UTF-8"?>
-<OME xmlns="{ns_ome_default}s" 
+<OME xmlns="{ns_ome_default}" 
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
-     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2012-03/ome.xsd">
+     xsi:schemaLocation="{ns_ome_default} {ns_ome_default}/ome.xsd">
   <Image ID="Image:0" Name="default.png">
-    <AcquiredDate>%(DEFAULT_NOW)s</AcquiredDate>
+    <AcquiredDate>{DEFAULT_NOW}</AcquiredDate>
     <Pixels DimensionOrder="XYCTZ" 
             ID="Pixels:0" 
             SizeC="1" 
@@ -48,12 +48,16 @@ def xsd_now():
 <Channel ID="Channel:0:0" SamplesPerPixel="1">
         <LightPath/>
       </Channel>
-      <BinData xmlns="%(NS_BINARY_FILE)s" 
+      <BinData xmlns="{ns_binary_file}" 
        BigEndian="false" Length="0"/>
     </Pixels>
   </Image>
-  <StructuredAnnotations xmlns="{ns_sa_default}s"/>
-</OME>""".format(ns_ome_default=NS_DEFAULT.format(ns_key='ome'), ns_sa_default=NS_DEFAULT.format(ns_key='sa'))
+  <StructuredAnnotations xmlns="{ns_sa_default}"/>
+</OME>""".format(
+             ns_ome_default=NS_DEFAULT.format(ns_key='OME'), 
+             ns_sa_default=NS_DEFAULT.format(ns_key='sa'),
+             ns_binary_file=NS_DEFAULT.format(ns_key="BinaryFile"),
+             DEFAULT_NOW=DEFAULT_NOW)
 
 #
 # These are the OME-XML pixel types - not all supported by subimager
diff --git a/bioformats/tests/test_omexml.py b/bioformats/tests/test_omexml.py
index f466785..39156ba 100644
--- a/bioformats/tests/test_omexml.py
+++ b/bioformats/tests/test_omexml.py
@@ -11,9 +11,11 @@
 
 import datetime
 import os
+import re
 import unittest
 import urllib
 import xml.dom
+import xml.etree.ElementTree
 
 import bioformats.omexml as O
 
@@ -32,6 +34,22 @@ def test_00_00_init(self):
         self.assertEquals(o.root_node.tag, O.qn(o.get_ns("ome"), "OME"))
         self.assertEquals(o.image_count, 1)
         
+    def test_00_01_ns_binary_file(self):
+        # regression test of issue #37
+        o = O.OMEXML()
+        xmlstr = o.to_xml()
+        tree = xml.etree.ElementTree.fromstring(xmlstr)
+        bfelements = tree.findall(".//*[@BigEndian]")
+        self.assertEqual(len(bfelements), 1)
+        #
+        # Try to find BinData with the namespace,
+        # http://www.openmicroscopy.org/Schemas/BinaryFile/YYYY-MM
+        #
+        match = re.match(
+            "\\{http://www.openmicroscopy.org/Schemas/BinaryFile/"
+            "\\d{4}-\\d{2}\\}BinData", bfelements[0].tag)
+        self.assertTrue(match is not None)
+        
     def test_01_01_read(self):
         for xml in (self.GROUPFILES_XML, TIFF_XML):
             o = O.OMEXML(xml)