Small improvements to scripts/grt/export.py for testing.

- Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this).
- Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell.

lib/galaxy/util/hash_util.py

@@ -10,11 +10,30 @@ import logging
 
 log = logging.getLogger(__name__)
 
+BLOCK_SIZE = 1024 * 1024
+
 sha1 = hashlib.sha1
+sha256 = hashlib.sha256
 sha = sha1
 md5 = hashlib.md5
 
 
+def memory_bound_hexdigest(hash_func, path=None, file=None):
+    hasher = hash_func()
+    if file is None:
+        assert path is not None
+        file = open(path, "rb")
+    else:
+        assert path is None, "Cannot specify path and path keyword arguments."
+
+    try:
+        for block in iter(lambda: file.read(BLOCK_SIZE), b''):
+                hasher.update(block)
+        return hasher.hexdigest()
+    finally:
+        file.close()
+
+
 def md5_hash_file(path):
     """
     Return a md5 hashdigest for a file or None if path could not be read.

scripts/grt/export.py

@@ -7,7 +7,6 @@ import argparse
 import json
 import logging
 import os
-import subprocess
 import sys
 import tarfile
 import time
@@ -21,6 +20,7 @@ import galaxy
 import galaxy.config
 from galaxy.model import mapping
 from galaxy.objectstore import build_object_store_from_config
+from galaxy.util import hash_util
 from galaxy.util.properties import load_app_properties
 
 sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml.sample'))
@@ -345,10 +345,8 @@ def main(argv):
         os.unlink(REPORT_BASE + '.' + name + '.tsv')
 
     _times.append(('job_finish', time.time() - _start_time))
-    sha = subprocess.check_output(['sha256sum', REPORT_BASE + '.tar.gz'])
+    sha = hash_util.memory_bound_hexdigest(hash_util.sha256, REPORT_BASE + ".tar.gz")
     _times.append(('hash_finish', time.time() - _start_time))
-    # Strip out to space
-    sha = sha[0:sha.index(' ')]
 
     # Now serialize the individual report data.
     with open(REPORT_BASE + '.json', 'w') as handle:

scripts/grt/grt.yml.sample

@@ -1,7 +1,3 @@
-# Location of your galaxy config file. The radio telescope will need to
-# partially initialize a copy of galaxy.
-galaxy_config: config/galaxy.ini
-
 grt:
     # Go to https://telescope.galaxyproject.org to obtain an Instance ID and API key
     instance_id: