1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8718607f7ae5/
changeset: 8718607f7ae5
user: dannon
date: 2011-12-09 16:19:20
summary: Update collect_child_datasets to work with ObjectStore.
affected #: 1 file
diff -r 187267753315c372a684a5170d053a6b561aebb5 -r 8718607f7ae5554b6a43caff974a4949eb504950 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1890,7 +1890,7 @@
sa_session=self.sa_session )
self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset )
# Move data from temp location to dataset location
- shutil.move( filename, child_dataset.file_name )
+ self.app.object_store.update_from_file(child_dataset.dataset.id, filename, create=True)
self.sa_session.add( child_dataset )
self.sa_session.flush()
child_dataset.set_size()
@@ -1902,7 +1902,7 @@
job = None
for assoc in outdata.creating_job_associations:
job = assoc.job
- break
+ break
if job:
assoc = self.app.model.JobToOutputDatasetAssociation( '__new_child_file_%s|%s__' % ( name, designation ), child_dataset )
assoc.job = job
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/3ccece0dbc02/
changeset: 3ccece0dbc02
user: dannon
date: 2011-12-09 13:01:31
summary: Job.fail() failure bugfix.
affected #: 1 file
diff -r 7611d5d306bb462c803b36d236cebf874ba9e1b8 -r 3ccece0dbc02812da682481bf1196d69bcc38d67 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -500,7 +500,7 @@
# If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
if self.tool:
self.tool.job_failed( self, message, exception )
- if self.app.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED):
+ if self.app.config.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED):
self.cleanup()
def change_state( self, state, info = False ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7f783a4889f7/
changeset: 7f783a4889f7
user: natefoo
date: 2011-12-08 23:34:19
summary: Object store bug fix (direct filesystem access in the default tool action)
affected #: 1 file
diff -r 8d668e1d51520f7663915ff5535852e47a7dd235 -r 7f783a4889f74bacf61a97a8e8d39ebda1cc9b9d lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -291,14 +291,11 @@
trans.sa_session.flush()
trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions )
# Create an empty file immediately
- # open( data.file_name, "w" ).close()
trans.app.object_store.create( data.id, store_name=store_name )
if not store_name_set:
# Ensure all other datasets in this job are created in the same store
store_name = trans.app.object_store.store_name( data.id )
store_name_set = True
- # Fix permissions
- util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 )
# This may not be neccesary with the new parent/child associations
data.designation = name
# Copy metadata from one of the inputs if requested.
https://bitbucket.org/galaxy/galaxy-central/changeset/95529ba09179/
changeset: 95529ba09179
user: natefoo
date: 2011-12-08 23:45:48
summary: Missing part of the last commit.
affected #: 1 file
diff -r 7f783a4889f74bacf61a97a8e8d39ebda1cc9b9d -r 95529ba09179dcd08da79f1c67151a138284e8b1 lib/galaxy/objectstore/__init__.py
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -204,6 +204,7 @@
def __init__(self, config, file_path=None, extra_dirs=None):
super(DiskObjectStore, self).__init__()
self.file_path = file_path or config.file_path
+ self.config = config
if extra_dirs is not None:
self.extra_dirs = extra_dirs
@@ -300,6 +301,7 @@
if not dir_only:
path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
open(path, 'w').close()
+ util.umask_fix_perms( path, self.config.umask, 0666 )
def empty(self, dataset_id, **kwargs):
return os.path.getsize(self.get_filename(dataset_id, **kwargs)) > 0
https://bitbucket.org/galaxy/galaxy-central/changeset/c6735493b09f/
changeset: c6735493b09f
user: natefoo
date: 2011-12-08 23:46:05
summary: Merge.
affected #: 1 file
diff -r 95529ba09179dcd08da79f1c67151a138284e8b1 -r c6735493b09f507e02564e6c79f9fef39d7bf7fa lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -224,7 +224,7 @@
int( self.value )
except:
raise ValueError( "An integer is required" )
- elif self.value is None:
+ elif self.value is None and not self.optional:
raise ValueError( "The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name )
self.min = elem.get( 'min' )
self.max = elem.get( 'max' )
@@ -296,7 +296,7 @@
float( self.value )
except:
raise ValueError( "A real number is required" )
- elif self.value is None:
+ elif self.value is None and not self.optional:
raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be a real number" )
if self.min:
try:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/75c27994fc9a/
changeset: 75c27994fc9a
user: dan
date: 2011-12-08 22:57:12
summary: Allow not specifying a value attribute for an optional tool parameter. Partially resolves #661.
affected #: 1 file
diff -r 8d668e1d51520f7663915ff5535852e47a7dd235 -r 75c27994fc9aa265bdecd6ad7962f0c4f51b3682 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -224,7 +224,7 @@
int( self.value )
except:
raise ValueError( "An integer is required" )
- elif self.value is None:
+ elif self.value is None and not self.optional:
raise ValueError( "The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name )
self.min = elem.get( 'min' )
self.max = elem.get( 'max' )
@@ -296,7 +296,7 @@
float( self.value )
except:
raise ValueError( "A real number is required" )
- elif self.value is None:
+ elif self.value is None and not self.optional:
raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be a real number" )
if self.min:
try:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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