Merge pull request #125 from jmchilton/md5

Allow testing tool outputs based on MD5 hashes.

lib/galaxy/tools/parser/xml.py

@@ -362,11 +362,13 @@ def __parse_test_attributes( output_elem, attrib ):
     metadata = {}
     for metadata_elem in output_elem.findall( 'metadata' ):
         metadata[ metadata_elem.get('name') ] = metadata_elem.get( 'value' )
-    if not (assert_list or file or extra_files or metadata):
-        raise Exception( "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, etc...)")
+    md5sum = attrib.get("md5", None)
+    if not (assert_list or file or extra_files or metadata or md5sum):
+        raise Exception( "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or md5 tests, etc...)")
     attributes['assert_list'] = assert_list
     attributes['extra_files'] = extra_files
     attributes['metadata'] = metadata
+    attributes['md5'] = md5sum
     return file, attributes
 
 

lib/galaxy/tools/test.py

@@ -133,6 +133,7 @@ class ToolTestBuilder( object ):
             self.stderr = test_dict.get("stderr", None)
             self.expect_exit_code = test_dict.get("expect_exit_code", None)
             self.expect_failure = test_dict.get("expect_failure", False)
+            self.md5 = test_dict.get("md5", None)
         except Exception, e:
             self.error = True
             self.exception = e

test/base/twilltestcase.py

@@ -2271,6 +2271,14 @@ class TwillTestCase( unittest.TestCase ):
                 errmsg = 'History item %s different than expected\n' % (hid)
                 errmsg += str( err )
                 raise AssertionError( errmsg )
+        if attributes is not None and attributes.get("md5", None) is not None:
+            md5 = attributes.get("md5")
+            try:
+                self._verify_md5(data, md5)
+            except AssertionError, err:
+                errmsg = 'History item %s different than expected\n' % (hid)
+                errmsg += str( err )
+                raise AssertionError( errmsg )
         if filename is not None:
             local_name = self.get_filename( filename, shed_tool_id=shed_tool_id )
             temp_name = self.makeTfname(fname=filename)
@@ -2323,6 +2331,18 @@ class TwillTestCase( unittest.TestCase ):
                 if 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
                     os.remove( temp_name )
 
+    def _verify_md5( self, data, expected_md5 ):
+        import md5
+        m = md5.new()
+        m.update( data )
+        actual_md5 = m.hexdigest()
+        if expected_md5 != actual_md5:
+            template = "Output md5sum [%s] does not match expected [%s]."
+            message = template % (actual_md5, expected_md5)
+            assert False, message
+
+
+
     def view_external_service( self, external_service_id, strings_displayed=[] ):
         self.visit_url( '%s/external_service/view_external_service?id=%s' % ( self.url, external_service_id ) )
         for check_str in strings_displayed:

test/functional/tools/md5sum.xml

@@ -0,0 +1,17 @@
+<tool id="md5sum" name="md5sum" version="1.0.0">
+    <command>
+        cp $input $output
+    </command>
+    <inputs>
+        <param name="input" type="data" format="txt" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="simple_line.txt" />
+            <output name="out_file1" md5="ac94233685713ce99d1e712b0023c381" />
+        </test>
+    </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -17,6 +17,7 @@
   <tool file="metadata.xml" />
   <tool file="metadata_bam.xml" />
   <tool file="detect_errors_aggressive.xml" />
+  <tool file="md5sum.xml" />
   <tool file="job_properties.xml" />
   <tool file="gzipped_inputs.xml" />
   <tool file="output_order.xml" />