[galaxy-commits] commit/galaxy-central: 3 new changesets

[Bitbucket]

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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