issue #6 - check for presence of OMERO classes before trying to use them

Author: Lee Kamentsky

bioformats/__init__.py

@@ -79,7 +79,7 @@
 # Omero
 
 from .formatreader import use_omero_credentials, set_omero_credentials, get_omero_credentials
-from .formatreader import set_omero_login_hook, omero_logout
+from .formatreader import set_omero_login_hook, omero_logout, has_omero_packages
 from .formatreader import K_OMERO_SERVER, K_OMERO_PORT, K_OMERO_USER, K_OMERO_SESSION_ID,\
          K_OMERO_PASSWORD, K_OMERO_CONFIG_FILE
 

bioformats/formatreader.py

@@ -26,13 +26,16 @@
 
 import logging
 logger = logging.getLogger(__name__)
+import errno
+import exceptions
 import numpy as np
 import os
 import sys
 import urllib
 import urllib2
 import shutil
 import tempfile
+import traceback
 
 import javabridge as jutil
 import bioformats
@@ -340,6 +343,32 @@ def __init__(self, rdr):
                                   'Set the name of the data file')
     return ReaderWrapper
 
+__has_omero_jars = None
+def has_omero_packages():
+    '''Return True if we can find the packages needed for OMERO
+    
+    In order to run OMERO, you'll need the OMERO client and ICE
+    on your class path (not supplied with python-bioformats and
+    specific to your server's version)
+    '''
+    global __has_omero_jars
+    if __has_omero_jars is None:
+        class_loader = jutil.static_call(
+            "java/lang/ClassLoader", "getSystemClassLoader",
+            "()Ljava/lang/ClassLoader;")
+        for klass in ("Glacier2.PermissionDeniedException", 
+                      "loci.ome.io.OmeroReader", "omero.client"):
+            try:
+                jutil.call(
+                    class_loader, "loadClass", 
+                    "(Ljava/lang/String;)Ljava/lang/Class;", klass)
+            except:
+                __has_omero_jars = False
+                break
+        else:
+            __has_omero_jars = True
+    return __has_omero_jars
+
 __omero_server = None
 __omero_username = None
 __omero_session_id = None
@@ -542,9 +571,6 @@ def __init__(self, path=None, url=None, perform_init=True):
                             omero_logout()
                             omero_login()
                         else:
-                            import errno
-                            import exceptions
-                            import traceback
                             logger.warn(e.message)
                             for line in traceback.format_exc().split("\n"):
                                 logger.warn(line)
@@ -581,6 +607,12 @@ def __init__(self, path=None, url=None, perform_init=True):
                 self.path = self.path.replace("/", os.path.sep)
             filename = os.path.split(path)[1]
 
+        if not os.path.isfile(self.path):
+            raise exceptions.IOError(
+                errno.ENOENT, 
+                "The file, \"%s\", does not exist." % path,
+                path)
+            
         self.stream = jutil.make_instance('loci/common/RandomAccessInputStream',
                                           '(Ljava/lang/String;)V', 
                                           self.path)
@@ -664,14 +696,11 @@ def init_reader(self):
         try:
             self.rdr.setId(self.path)
         except jutil.JavaException, e:
-            import errno
-            import exceptions
-            import traceback
             logger.warn(e.message)
             for line in traceback.format_exc().split("\n"):
                 logger.warn(line)
             je = e.throwable
-            if jutil.is_instance_of(
+            if has_omero_packages() and jutil.is_instance_of(
                 je, "Glacier2/PermissionDeniedException"):
                 # Handle at a higher level
                 raise

bioformats/tests/test_load_using_bioformats.py

@@ -5,6 +5,7 @@
 # Copyright (c) 2009-2014 Broad Institute
 # All rights reserved.
 
+import exceptions
 import os
 import unittest
 
@@ -30,4 +31,11 @@ def test_load_using_bioformats(self):
         image, scale = load_image(path, rescale=False,
                                   wants_max_intensity=True)
         print image.shape
+        
+    def test_file_not_found(self):
+        # Regression test of issue #6
+        path = os.path.join(os.path.dirname(__file__), 'Channel5-01-A-01.tif')
+        self.assertRaises(exceptions.IOError, 
+                          lambda :load_image(path))
+
 

docs/index.rst

@@ -121,6 +121,13 @@ Writing images
 OMERO
 =====
 
+Python-bioformats can load images from OMERO URLs. To do this, you'll need
+to put the JAR files for your OMERO server version onto your Java classpath
+when you start. For OMERO server 5.0.0, these are blitz.jar, common.jar,
+ice.jar, ice-glacier2.jar, ice-storm.jar and ice-grid.jar. You'll also need
+to use the matching version of the Bio-formats library for the OMERO release
+instead of the one included with python-bioformats.
+
 .. autofunction:: bioformats.use_omero_credentials
 .. autofunction:: bioformats.set_omero_credentials
 .. autofunction:: bioformats.get_omero_credentials