[hg] galaxy 3494: Fix for generated primary file when uploading ...

9 Mar 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/00aab7119686
changeset: 3494:00aab7119686
user:      Dan Blankenberg <dan@bx.psu.edu>
date:      Tue Mar 09 11:18:45 2010 -0500
description:
Fix for generated primary file when uploading composite files. Remove missing_meta method from Rgenetics type, it will inherit from data.Text though image.Html.

diffstat:

 lib/galaxy/datatypes/genetics.py        |  6 ------
 lib/galaxy/tools/parameters/grouping.py |  2 +-
 2 files changed, 1 insertions(+), 7 deletions(-)

diffs (28 lines):

diff -r a532f6d868a6 -r 00aab7119686 lib/galaxy/datatypes/genetics.py

--- a/lib/galaxy/datatypes/genetics.py	Tue Mar 09 09:48:00 2010 -0500
+++ b/lib/galaxy/datatypes/genetics.py	Tue Mar 09 11:18:45 2010 -0500
@@ -275,12 +275,6 @@
     allow_datatype_change = False
     file_ext = 'rgenetics'
 
-    def missing_meta( self, dataset=None, **kwargs):
-        """Checks for empty meta values"""
-        for key, value in dataset.metadata.items():
-            if not value:
-                return True
-        return False
     def generate_primary_file( self, dataset = None ):
         rval = ['<html><head><title>Rgenetics Galaxy Composite Dataset </title></head><p/>']
         rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
diff -r a532f6d868a6 -r 00aab7119686 lib/galaxy/tools/parameters/grouping.py
--- a/lib/galaxy/tools/parameters/grouping.py	Tue Mar 09 09:48:00 2010 -0500
+++ b/lib/galaxy/tools/parameters/grouping.py	Tue Mar 09 11:18:45 2010 -0500
@@ -288,7 +288,7 @@
             dataset_info = None
             if dataset.datatype.composite_type == 'auto_primary_file':
                 #replace sniff here with just creating an empty file
-                temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file() ), prefix='upload_auto_primary_file' )
+                temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file( dataset ) ), prefix='upload_auto_primary_file' )
                 dataset.primary_file = temp_name
                 dataset.space_to_tab = False
                 dataset.precreated_name = dataset.name = 'Uploaded Composite Dataset (%s)' % ( file_type )

    

Greg Von Kuster

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