Changeset 1602:531be9ea2486

Timestamp:

11/04/08 11:56:09 (2 months ago)

Author:

Greg Von Kuster <greg@bx.psu.edu>

branch:

default

Message:

Upload tool will now create a job record, no job queued though.

Files:

• lib/galaxy/tools/actions/upload.py (modified) (7 diffs)

lib/galaxy/tools/actions/upload.py

@@ -26 +26 @@
-        temp_name = ""
-        data_list = []
-
+
+
+
+
+
+
+
+
+
+
+
+
+
-        if 'local_filename' in dir( data_file ):
-            # Use the existing file
@@ -35 +47 @@
-                data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, dbkey, space_to_tab=space_to_tab ) )
-            except Exception, e:
-
+job, 
-        elif 'filename' in dir( data_file ):
-            try:
@@ -44 +56 @@
-                data_list.append( self.add_file( trans, temp_name, file_name, file_type, dbkey, space_to_tab=space_to_tab ) )
-            except Exception, e:
-
+job, 
-        if url_paste not in [ None, "" ]:
-            if url_paste.lower().find( 'http://' ) >= 0 or url_paste.lower().find( 'ftp://' ) >= 0:
@@ -55 +67 @@
-                            data_list.append( self.add_file( trans, temp_name, line, file_type, dbkey, info="uploaded url", space_to_tab=space_to_tab ) )
-                        except Exception, e:
-
+job, 
-            else:
-                is_valid = False
@@ -68 +80 @@
-                        data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, dbkey, info="pasted entry", space_to_tab=space_to_tab ) )
-                    except Exception, e:
-
+job, 
-                else:
-
+job, 
-        if self.empty:
-
+job, 
-        elif len( data_list ) < 1:
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
-        data = trans.app.model.HistoryDatasetAssociation( create_dataset = True )
-        data.name = err_code 
@@ -84 +103 @@
-        data.info = err_msg
-        data.file_size = 0
+        data.state = data.states.EMPTY
-        data.flush()
-        data.state = data.states.EMPTY
-        trans.history.add_dataset( data )
-        trans.app.model.flush()
+        # Indicate job failure by setting state and message
+        job.state = trans.app.model.Job.states.ERROR
+        job.info = err_msg
+        # If the failure is due to a Galaxy framework exception, save the traceback
+        job.flush()
+        log.debug( 'tool %s job id %d ended with errors' % ( job.tool_id, job.id ) )
+        trans.log_event( 'job id %d ended with errors' % job.id, tool_id=job.tool_id )
-        return dict( output=data )
-
@@ -276 +302 @@
-        return False
-
+def nice_size( size ):
+    """Returns a readably formatted string with the size"""
+    words = [ 'bytes', 'Kb', 'Mb', 'Gb' ]
+    try:
+        size = float( size )
+    except:
+        return '??? bytes'
+    for ind, word in enumerate( words ):
+        step  = 1024 ** ( ind + 1 )
+        if step > size:
+            size = size / float( 1024 ** ind )
+            out  = "%.1f %s" % ( size, word )
+            return out
+    return '??? bytes'
+
-class BadFileException( Exception ):
-    pass