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Fixes for i18n support - all charsets set to utf-8, now able to paste multi-byte chars in upload form, templates use utf-8 as output_charset, other miscellaneous fixes.

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This commit is contained in:
Greg Von Kuster
2009-03-20 02:49:30 -04:00
parent ad8f672677
commit 354d0447df
21 changed files with 60 additions and 59 deletions
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lib/galaxy/datatypes/sniff.py
+2 -1
View File
@@ -21,7 +21,8 @@ def stream_to_file( stream, suffix='', prefix='', dir=None, text=False ):
chunk = stream.read(1048576)
if not chunk:
break
os.write(fd, chunk)
# TODO: does this work on binary files?
os.write( fd, chunk.encode( "utf-8" ) )
os.close(fd)
return temp_name
lib/galaxy/tools/actions/upload.py
+13 -17
View File
@@ -105,7 +105,7 @@ class UploadToolAction( object ):
try:
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:
log.excception( 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) )
log.exception( 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) )
self.remove_tempfile( temp_name )
return self.upload_empty( trans, job, "Error:", str( e ) )
else:
@@ -146,12 +146,11 @@ class UploadToolAction( object ):
def add_file( self, trans, temp_name, file_name, file_type, dbkey, info=None, space_to_tab=False ):
data_type = None
# See if we have an empty file
if not os.path.getsize( temp_name ) > 0:
raise BadFileException( "you attempted to upload an empty file." )
# See if we have a gzipped file, which, if it passes our restrictions, we'll decompress on the fly.
# See if we have a gzipped file, which, if it passes our restrictions,
# we'll decompress on the fly.
is_gzipped, is_valid = self.check_gzip( temp_name )
if is_gzipped and not is_valid:
raise BadFileException( "you attempted to upload an inappropriate file." )
@@ -176,7 +175,7 @@ class UploadToolAction( object ):
shutil.move( uncompressed, temp_name )
file_name = file_name.rstrip( '.gz' )
data_type = 'gzip'
ext = ''
if not data_type:
# See if we have a zip archive
is_zipped, is_valid, test_ext = self.check_zip( temp_name )
@@ -193,30 +192,28 @@ class UploadToolAction( object ):
raise BadFileException( "you must manually set the 'File Format' to either 'Binseq.zip' or 'Txtseq.zip' when uploading zip files." )
data_type = 'zip'
ext = file_type
if not data_type:
if self.check_binary( temp_name ):
ext = file_name.split( "." )[1].strip().lower()
if not( ext == 'ab1' or ext == 'scf' ):
raise BadFileException( "you attempted to upload an inappropriate file." )
if ext == 'ab1' and file_type != 'ab1':
raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." )
elif ext == 'scf' and file_type != 'scf':
raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." )
parts = file_name.split( "." )
if len( parts ) > 1:
ext = parts[1].strip().lower()
if not( ext == 'ab1' or ext == 'scf' ):
raise BadFileException( "you attempted to upload an inappropriate file." )
if ext == 'ab1' and file_type != 'ab1':
raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." )
elif ext == 'scf' and file_type != 'scf':
raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." )
data_type = 'binary'
if not data_type:
# We must have a text file
if self.check_html( temp_name ):
raise BadFileException( "you attempted to upload an inappropriate file." )
if data_type != 'binary' and data_type != 'zip':
if space_to_tab:
self.line_count = sniff.convert_newlines_sep2tabs( temp_name )
else:
self.line_count = sniff.convert_newlines( temp_name )
if file_type == 'auto':
log.debug("In upload, in if file_type == 'auto':")
ext = sniff.guess_ext( temp_name, sniff_order=trans.app.datatypes_registry.sniff_order )
else:
ext = file_type
@@ -312,7 +309,6 @@ class UploadToolAction( object ):
if chunk is None:
temp.close()
return False
def check_binary( self, temp_name, chunk=None ):
if chunk is None:
temp = open( temp_name, "U" )
lib/galaxy/util/__init__.py
+2 -2
View File
@@ -107,9 +107,9 @@ def sanitize_text(text):
def sanitize_param(value):
"""Clean incoming parameters (strings or lists)"""
if type(value) == type('x'):
if isinstance( value, basestring ):
return sanitize_text(value)
elif type(value) == type([]):
elif isinstance( value, list ):
return map(sanitize_text, value)
else:
raise Exception, 'Unknown parameter type'
lib/galaxy/web/controllers/ucsc_proxy.py
+1 -1
View File
@@ -121,7 +121,7 @@ beginning = '''<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "h
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="/static/style/base.css" rel="stylesheet" type="text/css" />
<script language="javascript" type="text/javascript">
function changeTarget(target)
lib/galaxy/web/framework/__init__.py
+9 -4
View File
@@ -87,7 +87,8 @@ class WebApplication( base.WebApplication ):
self.mako_template_lookup = mako.lookup.TemplateLookup(
directories = [ galaxy_app.config.template_path ] ,
module_directory = galaxy_app.config.template_cache,
collection_size = 500 )
collection_size = 500,
output_encoding = 'utf-8' )
# Security helper
self.security = galaxy_app.security
def handle_controller_exception( self, e, trans, **kwargs ):
@@ -131,7 +132,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
# Default to English
locales = 'en'
t = Translations.load( dirname='locale', locales=locales, domain='ginga' )
self.template_context.update ( dict( _=t.gettext, n_=t.gettext, N_=t.ngettext ) )
self.template_context.update ( dict( _=t.ugettext, n_=t.ugettext, N_=t.ungettext ) )
@property
def sa_session( self ):
"""
@@ -465,10 +466,12 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
return self.fill_template_mako( filename, **kwargs )
else:
template = Template( file=os.path.join(self.app.config.template_path, filename),
searchList=[kwargs, self.template_context, dict(caller=self, t=self, h=webhelpers, util=util, request=self.request, response=self.response, app=self.app)] )
searchList=[kwargs, self.template_context, dict(caller=self, t=self, h=webhelpers, util=util, request=self.request, response=self.response, app=self.app)],
output_encoding='utf-8' )
return str( template )
def fill_template_mako( self, filename, **kwargs ):
template = self.webapp.mako_template_lookup.get_template( filename )
template.output_encoding = 'utf-8'
data = dict( caller=self, t=self, trans=self, h=webhelpers, util=util, request=self.request, response=self.response, app=self.app )
data.update( self.template_context )
data.update( kwargs )
@@ -477,7 +480,9 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
"""
Fill in a template, putting any keyword arguments on the context.
"""
template = Template( source=template_string, searchList=[context or kwargs, dict(caller=self)] )
template = Template( source=template_string,
searchList=[context or kwargs, dict(caller=self)],
output_encoding='utf-8' )
return str(template)
class FormBuilder( object ):
lib/galaxy/web/framework/base.py
+19 -19
View File
@@ -14,8 +14,10 @@ import pkg_resources;
pkg_resources.require( "Paste" )
pkg_resources.require( "Routes" )
pkg_resources.require( "flup" )
pkg_resources.require( "WebOb" )
import routes
import webob
# We will use some very basic HTTP/wsgi utilities from the paste library
from paste.request import parse_headers, get_cookies, parse_formvars
@@ -212,7 +214,7 @@ class DefaultWebTransaction( object ):
else:
return None
class Request( object ):
class Request( webob.Request ):
"""
Encapsulates an HTTP request.
"""
@@ -220,26 +222,24 @@ class Request( object ):
"""
Create a new request wrapping the WSGI environment `environ`
"""
self.environ = environ
## self.environ = environ
webob.Request.__init__( self, environ, charset='utf-8', decode_param_names=False )
# Properties that are computed and cached on first use
@lazy_property
def remote_host( self ):
try:
return socket.gethostbyname( self.environ['REMOTE_ADDR'] )
return socket.gethostbyname( self.remote_addr )
except socket.error:
return self.environ['REMOTE_ADDR']
@lazy_property
def headers( self ):
return dict( parse_headers( self.environ ) )
return self.remote_addr
@lazy_property
def cookies( self ):
return get_cookies( self.environ )
@lazy_property
def base( self ):
return ( self.scheme + "://" + self.environ['HTTP_HOST'] )
@lazy_property
def params( self ):
return parse_formvars( self.environ )
return ( self.scheme + "://" + self.host )
## @lazy_property
## def params( self ):
## return parse_formvars( self.environ )
@lazy_property
def path( self ):
return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO']
@@ -247,15 +247,15 @@ class Request( object ):
def browser_url( self ):
return self.base + self.path
# Descriptors that map properties to the associated environment
scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' )
remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' )
## scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' )
## remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' )
remote_port = WSGIEnvironmentProperty( 'REMOTE_PORT' )
method = WSGIEnvironmentProperty( 'REQUEST_METHOD' )
script_name = WSGIEnvironmentProperty( 'SCRIPT_NAME' )
## method = WSGIEnvironmentProperty( 'REQUEST_METHOD' )
## script_name = WSGIEnvironmentProperty( 'SCRIPT_NAME' )
protocol = WSGIEnvironmentProperty( 'SERVER_PROTOCOL' )
query_string = WSGIEnvironmentProperty( 'QUERY_STRING' )
path_info = WSGIEnvironmentProperty( 'PATH_INFO' )
## query_string = WSGIEnvironmentProperty( 'QUERY_STRING' )
## path_info = WSGIEnvironmentProperty( 'PATH_INFO' )
class Response( object ):
"""
Describes an HTTP response. Currently very simple since the actual body
@@ -298,7 +298,7 @@ class Response( object ):
return "%d %s" % ( exception.code, exception.title )
else:
return self.status
# ---- Utilities ------------------------------------------------------------
CHUNK_SIZE = 2**16
lib/galaxy/webapps/reports/templates/base_panels.mako
+1 -1
View File
@@ -31,7 +31,7 @@
<html lang="en">
<head>
<title>${self.title()}</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
${self.javascripts()}
${self.stylesheets()}
</head>
lib/galaxy/webapps/reports/templates/masthead.mako
+1 -1
View File
@@ -2,7 +2,7 @@
<html>
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<link href="${h.url_for('/static/style/masthead.css')}" rel="stylesheet" type="text/css" />
</head>
scripts/paster.py
-1
View File
@@ -7,7 +7,6 @@ top level directly.
import os, sys
sys.setdefaultencoding( 'utf_8' )
assert sys.version_info[:2] >= ( 2, 4 )
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
templates/base.mako
+1 -1
View File
@@ -4,7 +4,7 @@
<head>
<title>a ${self.title()}</title>
<meta http-equiv="Content-Type" content="text/html; charset=${_('iso-8859-1')}" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
${self.stylesheets()}
${self.javascripts()}
</head>
templates/base_panels.mako
+1 -1
View File
@@ -42,7 +42,7 @@
<html>
<head>
<title>${self.title()}</title>
<meta http-equiv="Content-Type" content="text/html; charset=${_('iso-8859-1')}" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
${self.javascripts()}
${self.stylesheets()}
</head>
templates/dataset/errors.tmpl
+1 -1
View File
@@ -2,7 +2,7 @@
<html>
<head>
<title>Dataset generation errors</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="/static/style/base.css" rel="stylesheet" type="text/css" />
<style>
pre
templates/dataset/validation.tmpl
+1 -1
View File
@@ -3,7 +3,7 @@
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="/static/style/base.css" rel="stylesheet" type="text/css" />
<script type="text/javascript" src="/static/universe.js">var dummy1=0;</script>
</head>
templates/root/history.mako
+1 -1
View File
@@ -11,7 +11,7 @@
<!-- running: do not change this comment, used by TwillTestCase.wait -->
%endif
<meta http-equiv="Content-Type" content="text/html; charset=${_('iso-8859-1')}" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta http-equiv="Pragma" content="no-cache">
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<link href="${h.url_for('/static/style/history.css')}" rel="stylesheet" type="text/css" />
templates/root/masthead.mako
+1 -1
View File
@@ -5,7 +5,7 @@
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=${_('iso-8859-1')}" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<link href="${h.url_for('/static/style/masthead.css')}" rel="stylesheet" type="text/css" />
</head>
templates/root/tool_menu.mako
+1 -1
View File
@@ -49,7 +49,7 @@
<html>
<head>
<title>${_('Galaxy Tools')}</title>
<meta http-equiv="Content-Type" content="text/html; charset=${_('iso-8859-1')}" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" />
templates/tool_executed.mako
+1 -1
View File
@@ -3,7 +3,7 @@
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<script type="text/javascript">
var inside_galaxy_frameset = false;
templates/tool_form.mako
+1 -1
View File
@@ -9,7 +9,7 @@ from galaxy.util.expressions import ExpressionContext
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
<script type='text/javascript' src="${h.url_for('/static/scripts/jquery.js')}"> </script>
<script type="text/javascript">
templates/workflow/build_from_current_history.mako
+1 -1
View File
@@ -6,7 +6,7 @@
<head>
<title>Galaxy</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link href="${h.url_for('/static/style/history.css')}" rel="stylesheet" type="text/css" />
<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
tools/data_source/wormbase.xml
+1 -1
View File
@@ -2,7 +2,7 @@
<tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="post">
<description>server</description>
<command interpreter="python">data_source.py $output</command>
<inputs action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top">
<inputs action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" target="_top">
<display>go to Wormbase server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" />
</inputs>
tools/data_source/wormbase_test.xml
+1 -1
View File
@@ -2,7 +2,7 @@
<tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="post">
<description>test server</description>
<command interpreter="python">data_source.py $output</command>
<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top">
<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" target="_top">
<display>go to Wormbase test server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" />
</inputs>