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fix for errors thrown when requested underlying file of dataset does not exist; even better exception handling for ldda-archive downloading

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This commit is contained in:
Martin Cech
2013-12-17 15:58:40 -05:00
parent 1347121230
commit 4c93c9b03d
2 changed files with 48 additions and 11 deletions
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lib/galaxy/util/streamball.py
+7 -2
View File
@@ -3,6 +3,7 @@ A simple wrapper for writing tarballs as a stream.
"""
import os
import logging, tarfile
from galaxy.exceptions import ObjectNotFound
log = logging.getLogger( __name__ )
@@ -14,8 +15,12 @@ class StreamBall( object ):
self.mode = mode
self.wsgi_status = None
self.wsgi_headeritems = None
def add( self, file, relpath ):
self.members[file] = relpath
def add( self, file, relpath, check_file=False):
if check_file and len(file)>0:
if not os.path.isfile(file):
raise ObjectNotFound
else:
self.members[file] = relpath
def stream( self, environ, start_response ):
response_write = start_response( self.wsgi_status, self.wsgi_headeritems )
class tarfileobj:
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+41 -9
View File
@@ -14,7 +14,7 @@ import urllib
import urllib2
import zipfile
from paste.httpexceptions import HTTPBadRequest
from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException
from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound
from galaxy.security import Action
from galaxy import util, web
from galaxy.util.streamball import StreamBall
@@ -84,7 +84,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
return 'error of unknown kind' + str( e )
if format in [ 'zip','tgz','tbz' ]:
error = False
# error = False
killme = string.punctuation + string.whitespace
trantab = string.maketrans(killme,'_'*len(killme))
try:
@@ -117,12 +117,12 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] )
trans.response.status = 500
return "Unable to create archive for download, please report - %s" % sys.exc_info()[0]
if not error:
if True:
composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
seen = []
for ldda in lddas:
if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]:
continue
# if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]:
# continue
ext = ldda.extension
is_composite = ext in composite_extensions
path = ""
@@ -135,6 +135,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
path = os.path.join( parent_folder.name, path )
parent_folder = parent_folder.parent
path += ldda.name
while path in seen:
path += '_'
seen.append( path )
@@ -145,30 +146,61 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
if zpathext == '':
zpath = '%s.html' % zpath # fake the real nature of the html file
try:
archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set
if format=='zip':
archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set
else:
archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
except IOError:
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name)
trans.response.status = 500
return "Unable to create archive for download, please report this error"
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
trans.response.status = 500
return "Requested dataset does not exist on the host."
except:
trans.response.status = 500
return "Unknown error, please report this error"
flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths
for fpath in flist:
efp,fname = os.path.split(fpath)
if fname > '':
fname = fname.translate(trantab)
try:
archive.add( fpath,fname )
if format=='zip':
archive.add( fpath,fname )
else:
archive.add( fpath,fname, check_file=True )
except IOError:
log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname))
trans.response.status = 500
return "Unable to create archive for download, please report this error"
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % fpath )
trans.response.status = 500
return "Requested dataset does not exist on the host."
except:
trans.response.status = 500
return "Unknown error, please report this error"
else: # simple case
try:
archive.add( ldda.dataset.file_name, path )
if format=='zip':
archive.add( ldda.dataset.file_name, path )
else:
archive.add( ldda.dataset.file_name, path, check_file=True )
except IOError:
log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name)
trans.response.status = 500
return "Unable to create archive for download, please report this error"
if not error:
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
trans.response.status = 500
return "Requested dataset does not exist on the host."
except:
trans.response.status = 500
return "Unknown error, please report this error"
if True:
lname = 'selected_dataset'
fname = lname.replace( ' ', '_' ) + '_files'
if format == 'zip':