details: http://www.bx.psu.edu/hg/galaxy/rev/e2d37ea1a436 changeset: 2705:e2d37ea1a436 user: Nate Coraor nate@bx.psu.edu date: Wed Sep 16 15:30:17 2009 -0400 description: merge
0 file(s) affected in this change:
diffs (39 lines):
diff -r fc1be2626130 -r e2d37ea1a436 eggs.ini --- a/eggs.ini Wed Sep 16 15:19:35 2009 -0400 +++ b/eggs.ini Wed Sep 16 15:30:17 2009 -0400 @@ -23,7 +23,6 @@ python_lzo = 1.08 threadframe = 0.2 guppy = 0.1.8 -numpy = 1.2.1
[eggs:noplatform] Beaker = 1.4 @@ -63,7 +62,6 @@
; source location, necessary for scrambling [source] -numpy = http://downloads.sourceforge.net/numpy/numpy-1.2.1.tar.gz bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.... DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz diff -r fc1be2626130 -r e2d37ea1a436 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Wed Sep 16 15:19:35 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Wed Sep 16 15:30:17 2009 -0400 @@ -495,8 +495,14 @@ shutil.move( dataset_path.false_path, dataset_path.real_path ) log.debug( "finish(): Moved %s to %s" % ( dataset_path.false_path, dataset_path.real_path ) ) except ( IOError, OSError ): - self.fail( "Job %s's output dataset(s) could not be read" % job.id ) - return + # this can happen if Galaxy is restarted during the job's + # finish method - the false_path file has already moved, + # and when the job is recovered, it won't be found. + if os.path.exists( dataset_path.real_path ) and os.stat( dataset_path.real_path ).st_size > 0: + log.warning( "finish(): %s not found, but %s is not empty, so it will be used instead" % ( dataset_path.false_path, dataset_path.real_path ) ) + else: + self.fail( "Job %s's output dataset(s) could not be read" % job.id ) + return job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) ) for dataset_assoc in job.output_datasets: context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset )