Hi all,

While testing a BLAST search using plain text output (the 'txt'
datatype in Galaxy) or subclasses (like 'blastxml') using galaxy-dist
with task splitting enabled, I found I new bug when the files are
merged:

Error merging files global name 'shutil' is not defined

This is a side effect of this commit due to a missing import
(perhaps the imports changed since Bjoern wrote the patch):
https://bitbucket.org/galaxy/galaxy-central/commits/510b063792de89332428ed12ea1025155a7769c9

In addition to the missing import in data.py, there is a potential
similar issue with binary.py but this is masked by an evil
import * line ;)

My suggested patch for the import issue below, however right
now even though the merge is failing, Galaxy failed to treat
the job as a failure - it was shown as a green successful job
with "Error merging files" as stdout, and for stderr:
 "global name 'shutil' is not defined", but return code 0.

So there is a deeper problem with the merge error not marking
the job as failed.

Also there is a minor bug in that the stdout and stderr are
combined for the peep text without any white space -
presumably most of the time the stdout will have a trailing
new line, but not here - thus "filesglobal" [sic], not say
"files global" or a newline. There's a second patch below
for that minor issue too (although it seems my new lines
get turned into spaces by the time they are shown in
the history peep text).

Regards,

Peter

--

$ hg diff
diff -r 8b9ca63f9128 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py    Wed Apr 24 16:24:41 2013 -0400
+++ b/lib/galaxy/datatypes/binary.py    Thu Apr 25 11:32:51 2013 +0100
@@ -12,7 +12,7 @@
 from bx.seq.twobit import TWOBIT_MAGIC_NUMBER,
TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE
 from urllib import urlencode, quote_plus
 import zipfile, gzip
-import os, subprocess, tempfile
+import os, subprocess, tempfile, shutil
 import struct

 log = logging.getLogger(__name__)
diff -r 8b9ca63f9128 lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py    Wed Apr 24 16:24:41 2013 -0400
+++ b/lib/galaxy/datatypes/data.py    Thu Apr 25 11:32:51 2013 +0100
@@ -3,6 +3,7 @@
 import mimetypes
 import os
 import sys
+import shutil
 import tempfile
 import zipfile
 from cgi import escape




$ hg diff
diff -r 8b9ca63f9128 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py       Wed Apr 24 16:24:41 2013 -0400
+++ b/lib/galaxy/jobs/__init__.py       Thu Apr 25 11:43:30 2013 +0100
@@ -924,7 +924,13 @@
             for dataset in
dataset_assoc.dataset.dataset.history_associations +
dataset_assoc.dataset.dataset.library_associations: #need to update
all associated output hdas, i.e. history was shared with job running
                 dataset.blurb = 'done'
                 dataset.peek  = 'no peek'
-                dataset.info = ( dataset.info  or '' ) +
context['stdout'] + context['stderr']
+                dataset.info = (dataset.info or '')
+                if context['stdout'].strip():
+                    #Ensure white space between entries
+                    dataset.info = dataset.info.rstrip() + "\n" +
context['stdout'].strip()
+                if context['stderr'].strip():
+                    #Ensure white space between entries
+                    dataset.info = dataset.info.rstrip() + "\n" +
context['stderr'].strip()
                 dataset.tool_version = self.version_string
                 dataset.set_size()
                 if 'uuid' in context:
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