From 2ddab5819a7327ef09fb5533aece984d9dfe7f59 Mon Sep 17 00:00:00 2001
From: Ian Schenck <ian@bx.psu.edu>
Date: Fri, 9 Mar 2007 19:45:29 +0000
Subject: [PATCH] Script that will run like a tool for each dataset generated. 
 Is this in the right place?  P.S. this stuff isn't final.

---
 scripts/validate.py | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 scripts/validate.py

diff --git a/scripts/validate.py b/scripts/validate.py
new file mode 100644
index 00000000000..97f911d1030
--- /dev/null
+++ b/scripts/validate.py
@@ -0,0 +1,39 @@
+#!/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
+    -c, --cols=N,N,N,N: column metadata, in the case of GFF, BED, or intervals
+    -x, --ext=N: extension as understood by galaxy
+"""
+from 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.cols:
+        cols = options.cols.split(",")
+        data.metadata.chromCol = cols[0]
+        data.metadata.startCol = cols[1]
+        data.metadata.endCol = cols[2]
+        data.metadata.strandCol = cols[3]
+
+    errors = data.datatype.validate( data )
+    print util.object_to_string(errors)
+
+if __name__ == "__main__":
+    main()