Revert 2715.

lib/galaxy/config.py

@@ -31,8 +31,6 @@ class Configuration( object ):
         # Where dataset files are stored
         self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
         self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
-        # Directory to be used when creating temporary files ( generally from tools )
-        self.tmp_file_path = resolve_path( kwargs.get( "tmp_file_path", "/tmp" ), self.root )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )

lib/galaxy/datatypes/data.py

@@ -223,10 +223,10 @@ class Data( object ):
 
 class Text( Data ):
 
-    def write_from_stream( self, dataset, stream, directory=None ):
+    def write_from_stream(self, dataset, stream):
         """Writes data from a stream"""
         # write it twice for now 
-        fd, temp_name = tempfile.mkstemp( dir=directory )
+        fd, temp_name = tempfile.mkstemp()
         while 1:
             chunk = stream.read(1048576)
             if not chunk:
@@ -241,9 +241,9 @@ class Text( Data ):
             fp.write(line)
         fp.close()
 
-    def set_raw_data( self, dataset, data, directory=None ):
+    def set_raw_data(self, dataset, data):
         """Saves the data on the disc"""
-        fd, temp_name = tempfile.mkstemp( dir=directory )
+        fd, temp_name = tempfile.mkstemp()
         os.write(fd, data)
         os.close(fd)
 

lib/galaxy/datatypes/sniff.py

@@ -12,11 +12,11 @@ def get_test_fname(fname):
     full_path = os.path.join(path, 'test', fname)
     return full_path
 
-def stream_to_file( stream, directory=None ):
+def stream_to_file(stream):
     """
     Writes a stream to a temporary file, returns the temporary file's name
     """
-    fd, temp_name = tempfile.mkstemp( dir=directory )
+    fd, temp_name = tempfile.mkstemp()
     while 1:
         chunk = stream.read(1048576)
         if not chunk:
@@ -25,7 +25,7 @@ def stream_to_file( stream, directory=None ):
     os.close(fd)
     return temp_name
 
-def convert_newlines( fname, directory=None ):
+def convert_newlines( fname ):
     """
     Converts in place a file from universal line endings 
     to Posix line endings.
@@ -37,7 +37,7 @@ def convert_newlines( fname, directory=None ):
     >>> file(fname).read()
     '1 2\\n3 4\\n'
     """
-    fd, temp_name = tempfile.mkstemp( dir=directory )
+    fd, temp_name = tempfile.mkstemp()
     fp = os.fdopen( fd, "wt" )
     for i, line in enumerate( file( fname, "U" ) ):
         fp.write( "%s\n" % line.rstrip( "\r\n" ) )
@@ -46,7 +46,7 @@ def convert_newlines( fname, directory=None ):
     # Return number of lines in file.
     return i + 1
 
-def sep2tabs( fname, patt="\\s+", directory=None ):
+def sep2tabs(fname, patt="\\s+"):
     """
     Transforms in place a 'sep' separated file to a tab separated one
 
@@ -58,7 +58,7 @@ def sep2tabs( fname, patt="\\s+", directory=None ):
     '1\\t2\\n3\\t4\\n'
     """
     regexp = re.compile( patt )
-    fd, temp_name = tempfile.mkstemp( dir=directory )
+    fd, temp_name = tempfile.mkstemp()
     fp = os.fdopen( fd, "wt" )
     for i, line in enumerate( file( fname ) ):
         line  = line.rstrip( '\r\n' )
@@ -69,7 +69,7 @@ def sep2tabs( fname, patt="\\s+", directory=None ):
     # Return number of lines in file.
     return i + 1
 
-def convert_newlines_sep2tabs( fname, patt="\\s+", directory=None ):
+def convert_newlines_sep2tabs( fname, patt="\\s+" ):
     """
     Combines above methods: convert_newlines() and sep2tabs()
     so that files do not need to be read twice
@@ -82,7 +82,7 @@ def convert_newlines_sep2tabs( fname, patt="\\s+", directory=None ):
     '1\\t2\\n3\\t4\\n'
     """
     regexp = re.compile( patt )
-    fd, temp_name = tempfile.mkstemp( dir=directory )
+    fd, temp_name = tempfile.mkstemp()
     fp = os.fdopen( fd, "wt" )
     for i, line in enumerate( file( fname, "U" ) ):
         line  = line.rstrip( '\r\n' )

lib/galaxy/model/__init__.py

@@ -174,7 +174,6 @@ class Dataset( object ):
                     EMPTY = 'empty',
                     ERROR = 'error',
                     DELETED = 'deleted')
-    # The following is used for functional tests
     file_path = "/tmp/"
     engine = None
     def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, 

lib/galaxy/tools/__init__.py

@@ -985,8 +985,6 @@ class Tool:
         param_dict['__new_file_path__'] = os.path.abspath(self.app.config.new_file_path)
         # The following points to location (xxx.loc) files which are pointers to locally cached data
         param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path
-        # Directory to be used when creating temporary files ( generally from tools )
-        param_dict['GALAXY_TMP_FILE_DIR'] = self.app.config.tmp_file_path
         # Return the dictionary of parameters
         return param_dict
     

lib/galaxy/tools/actions/upload.py

@@ -79,8 +79,7 @@ class UploadToolAction( object ):
 
     def add_file( self, trans, file_obj, file_name, file_type, dbkey, info=None, space_to_tab=False ):
         data_type = None
-        tmp_file_path = trans.app.config.tmp_file_path
-        temp_name = sniff.stream_to_file( file_obj, directory=tmp_file_path )
+        temp_name = sniff.stream_to_file( file_obj )
         
         # See if we have an empty file
         if not os.path.getsize( temp_name ) > 0:
@@ -93,7 +92,7 @@ class UploadToolAction( object ):
         elif is_gzipped and is_valid:
             #We need to decompress the temp_name file
             CHUNK_SIZE = 2**20 # 1Mb   
-            fd, uncompressed = tempfile.mkstemp( dir=tmp_file_path )   
+            fd, uncompressed = tempfile.mkstemp()   
             gzipped_file = gzip.GzipFile( temp_name )
             while 1:
                 try:
@@ -147,7 +146,7 @@ class UploadToolAction( object ):
 
         if data_type != 'binary' and data_type != 'zip':
             if space_to_tab:
-                self.line_count = sniff.convert_newlines_sep2tabs( temp_name, directory=tmp_file_path )
+                self.line_count = sniff.convert_newlines_sep2tabs( temp_name )
             else:
                 self.line_count = sniff.convert_newlines( temp_name )
             if file_type == 'auto':

lib/galaxy/tools/util/maf_utilities.py

@@ -143,7 +143,7 @@ def maf_index_by_uid( maf_uid, index_location_file ):
     return None
 
 #builds and returns (index, index_filename) for specified maf_file
-def build_maf_index( maf_file, species=None, directory=None ):
+def build_maf_index( maf_file, species = None ):
     indexes = bx.interval_index_file.Indexes()
     try:
         maf_reader = bx.align.maf.Reader( open( maf_file ) )
@@ -156,7 +156,7 @@ def build_maf_index( maf_file, species=None, directory=None ):
                 if species is not None and c.src.split( "." )[0] not in species:
                     continue
                 indexes.add( c.src, c.forward_strand_start, c.forward_strand_end, pos )
-        fd, index_filename = tempfile.mkstemp( dir=directory )
+        fd, index_filename = tempfile.mkstemp()
         out = os.fdopen( fd, 'w' )
         indexes.write( out )
         out.close()