diff tools/validation/validate.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/validation/validate.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+
+"""
+Validate a dataset based on extension a metadata passed in on the
+command line.  Outputs a binhex'd representation of the exceptions.
+
+usage: %prog input output
+    -m, --metadata=N: base64 pickeled metadata
+    -x, --ext=N: extension as understood by galaxy
+"""
+
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+
+from galaxy import model
+from fileinput import FileInput
+from galaxy import util
+
+def main():
+    options, args = doc_optparse.parse( __doc__ )
+
+    try:
+        extension = options.ext
+    except:
+        doc_optparse.exception()
+
+    # create datatype
+    data = model.Dataset( extension=extension, id=int( args[0] ) )
+    data.file_path = "/home/ian/trunk/database/files/"
+    
+    if options.metadata:
+        data.metadata = util.string_to_object( options.metadata )
+
+    errors = data.datatype.validate( data )
+    print util.object_to_string(errors)
+
+if __name__ == "__main__":
+    main()