details:
http://www.bx.psu.edu/hg/galaxy/rev/f0a17cdd31a9
changeset: 2651:f0a17cdd31a9
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Fri Aug 28 15:55:37 2009 -0400
description:
merge
0 file(s) affected in this change:
diffs (152 lines):
diff -r e383b1e2f8b0 -r f0a17cdd31a9 eggs.ini
--- a/eggs.ini Fri Aug 28 15:44:28 2009 -0400
+++ b/eggs.ini Fri Aug 28 15:55:37 2009 -0400
@@ -26,13 +26,12 @@
numpy = 1.2.1
[eggs:noplatform]
-Beaker = 0.5
+Beaker = 1.4
docutils = 0.4
elementtree = 1.2.6_20050316
-flup = 0.5
lrucache = 0.2
;lsprof - james
-Mako = 0.1.10
+Mako = 0.2.4
MyghtyUtils = 0.52
nose = 0.9.1
NoseHTML = 0.2
@@ -76,12 +75,11 @@
python_lzo =
http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.t...
http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz
threadframe =
http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz
guppy =
http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz
-Beaker =
http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-0.5.tar.gz
+Beaker =
http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz
docutils =
http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz
elementtree =
http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz
-flup =
http://www.saddi.com/software/flup/dist/archive/flup-r2311.tar.gz
lrucache =
http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz
-Mako =
http://www.makotemplates.org/downloads/Mako-0.1.10.tar.gz
+Mako =
http://www.makotemplates.org/downloads/Mako-0.2.4.tar.gz
MyghtyUtils =
http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0....
nose =
http://www.somethingaboutorange.com/mrl/projects/nose/nose-0.9.1.tar.gz
NoseHTML =
http://dist.g2.bx.psu.edu/nosehtml-0.2.tar.bz2
diff -r e383b1e2f8b0 -r f0a17cdd31a9 lib/galaxy/datatypes/images.py
--- a/lib/galaxy/datatypes/images.py Fri Aug 28 15:44:28 2009 -0400
+++ b/lib/galaxy/datatypes/images.py Fri Aug 28 15:55:37 2009 -0400
@@ -9,6 +9,7 @@
from galaxy.datatypes.sniff import *
from urllib import urlencode, quote_plus
import zipfile
+import os, subprocess, tempfile
log = logging.getLogger(__name__)
@@ -240,6 +241,26 @@
"""Class describing a BAM binary file"""
file_ext = "bam"
MetadataElement( name="bam_index", desc="BAM Index File",
param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True )
+ def init_meta( self, dataset, copy_from=None ):
+ data.Binary.init_meta( self, dataset, copy_from=copy_from )
+ def set_meta( self, dataset, overwrite = True, **kwd ):
+ """
+ Sets index for BAM file.
+ """
+ index_file = dataset.metadata.bam_index
+ if not index_file:
+ index_file = dataset.metadata.spec['bam_index'].param.new_file(
dataset = dataset )
+ tmp_dir = tempfile.gettempdir()
+ tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir)
+ try:
+ subprocess.check_call(['cd', tmp_dir], shell=True)
+ subprocess.check_call('cp %s %s' % (dataset.file_name, tmpf1.name),
shell=True)
+ subprocess.check_call('samtools index %s' % tmpf1.name, shell=True)
+ subprocess.check_call('cp %s.bai %s' % (tmpf1.name,
index_file.file_name), shell=True)
+ except subprocess.CalledProcessError:
+ sys.stderr.write('There was a problem creating the index for the BAM
file\n')
+ tmpf1.close()
+ dataset.metadata.bam_index = index_file
def set_peek( self, dataset ):
if not dataset.dataset.purged:
export_url = "/history_add_to?" +
urlencode({'history_id':dataset.history_id,'ext':'bam','name':'bam
alignments','info':'Alignments file','dbkey':dataset.dbkey})
@@ -256,4 +277,3 @@
def get_mime(self):
"""Returns the mime type of the datatype"""
return 'application/octet-stream'
-
\ No newline at end of file
diff -r e383b1e2f8b0 -r f0a17cdd31a9 lib/galaxy/web/buildapp.py
--- a/lib/galaxy/web/buildapp.py Fri Aug 28 15:44:28 2009 -0400
+++ b/lib/galaxy/web/buildapp.py Fri Aug 28 15:55:37 2009 -0400
@@ -11,7 +11,6 @@
from paste.util import import_string
from paste import httpexceptions
from paste.deploy.converters import asbool
-import flup.middleware.session as flup_session
import pkg_resources
log = logging.getLogger( __name__ )
@@ -116,17 +115,6 @@
from paste import recursive
app = recursive.RecursiveMiddleware( app, conf )
log.debug( "Enabling 'recursive' middleware" )
- ## # Session middleware puts a session factory into the environment
- ## if asbool( conf.get( 'use_session', True ) ):
- ## store = flup_session.MemorySessionStore()
- ## app = flup_session.SessionMiddleware( store, app )
- ## log.debug( "Enabling 'flup session' middleware" )
- # Beaker session middleware
- if asbool( conf.get( 'use_beaker_session', False ) ):
- pkg_resources.require( "Beaker" )
- import beaker.session
- app = beaker.session.SessionMiddleware( app, conf )
- log.debug( "Enabling 'beaker session' middleware" )
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance
diff -r e383b1e2f8b0 -r f0a17cdd31a9 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Fri Aug 28 15:44:28 2009 -0400
+++ b/lib/galaxy/web/framework/__init__.py Fri Aug 28 15:55:37 2009 -0400
@@ -583,12 +583,12 @@
data.update( kwargs )
## return template.render( **data )
def render( environ, start_response ):
- response_write = start_response( self.response.wsgi_status(),
- self.response.wsgi_headeritems() )
- class C:
- def write( self, *args, **kwargs ):
- response_write( *args, **kwargs )
- context = mako.runtime.Context( C(), **data )
+ response_write = start_response( self.response.wsgi_status(),
self.response.wsgi_headeritems() )
+ class StreamBuffer( object ):
+ def write( self, d ):
+ response_write( d.encode( 'utf-8' ) )
+ buffer = StreamBuffer()
+ context = mako.runtime.Context( buffer, **data )
template.render_context( context )
return []
return render
diff -r e383b1e2f8b0 -r f0a17cdd31a9 lib/galaxy/web/framework/base.py
--- a/lib/galaxy/web/framework/base.py Fri Aug 28 15:44:28 2009 -0400
+++ b/lib/galaxy/web/framework/base.py Fri Aug 28 15:55:37 2009 -0400
@@ -13,7 +13,6 @@
import pkg_resources;
pkg_resources.require( "Paste" )
pkg_resources.require( "Routes" )
-pkg_resources.require( "flup" )
pkg_resources.require( "WebOb" )
import routes
diff -r e383b1e2f8b0 -r f0a17cdd31a9 templates/root/history_common.mako
--- a/templates/root/history_common.mako Fri Aug 28 15:44:28 2009 -0400
+++ b/templates/root/history_common.mako Fri Aug 28 15:55:37 2009 -0400
@@ -35,7 +35,7 @@
<a class="icon-button delete" title="delete"
href="${h.url_for( action='delete', id=data.id,
show_deleted_on_refresh=show_deleted_on_refresh )}"
id="historyItemDeleter-${data.id}"></a>
</div>
<span class="state-icon"></span>
- <span class="historyItemTitle"><b>${hid}:
${data.display_name()}</b></span>
+ <span class="historyItemTitle"><b>${hid}:
${data.display_name().decode('utf-8')}</b></span>
</div>
## Body for history items, extra info and actions, data "peek"