Bug#524180: bioruby: new upstream version 1.3.0 available

2009-04-15 Thread Naohisa GOTO
Package: bioruby
Severity: wishlist

New version of BioRuby 1.3.0 have been available since February 2009,
Currently packaged version is 1.1.0 which is outdated.
Please package the new version.




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Bug#502535: libruby1.8: REXML DoS fix causes error when parsing XML

2008-10-17 Thread Naohisa Goto
Package: libruby1.8
Version: 1.8.5-4etch3
Severity: normal

After libruby1.8 1.8.5-4etch3, parsing of some XML documents failed.
For example,

% ruby -r rexml/document -r open-uri -e 
'REXML::Document.new(URI.parse("http://github.com/bioruby/bioruby/tree/master%2Ftest%2Fdata%2Fblast%2Fb0002.faa.m7?raw=true";).read).root.each_element_with_text
 { |e| p e.name }'
"BlastOutput_program"
"BlastOutput_version"
/usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method 
`record_entity_expansion' for nil:NilClass (NoMethodError)
from /usr/lib/ruby/1.8/rexml/doctype.rb:143:in `entity'
from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize'
from /usr/lib/ruby/1.8/rexml/text.rb:321:in `each'
from /usr/lib/ruby/1.8/rexml/text.rb:321:in `unnormalize'
from /usr/lib/ruby/1.8/rexml/text.rb:173:in `value'
from /usr/lib/ruby/1.8/rexml/element.rb:457:in `text'
from /usr/lib/ruby/1.8/rexml/element.rb:438:in `has_text?'
from /usr/lib/ruby/1.8/rexml/element.rb:389:in `each_element_with_text'
from /usr/lib/ruby/1.8/rexml/element.rb:734:in `call'
from /usr/lib/ruby/1.8/rexml/element.rb:734:in `each_with_something'
from /usr/lib/ruby/1.8/rexml/element.rb:939:in `each'
from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each'
from /usr/lib/ruby/1.8/rexml/element.rb:939:in `each'
from /usr/lib/ruby/1.8/rexml/element.rb:733:in `each_with_something'
from /usr/lib/ruby/1.8/rexml/element.rb:393:in `each_element_with_text'
from -e:1

With 1.8.5-4etch2, no error occurred.

% ruby -r rexml/document -r open-uri -e 
'REXML::Document.new(URI.parse("http://github.com/bioruby/bioruby/tree/master%2Ftest%2Fdata%2Fblast%2Fb0002.faa.m7?raw=true";).read).root.each_element_with_text
 { |e| p e.name }'
"BlastOutput_program"
"BlastOutput_version"
"BlastOutput_reference"
"BlastOutput_db"
"BlastOutput_query-ID"
"BlastOutput_query-def"
"BlastOutput_query-len"
"BlastOutput_param"
"BlastOutput_iterations"

The same problem is reported in a blog.
http://mashing-it-up.blogspot.com/2008/09/dos-vulnerability-in-rexml-patch-fix.html

Following patch can fix this bug.

--- /usr/lib/ruby/1.8/rexml/entity.rb.ORIG  2008-10-11 04:35:02.0 
+0900
+++ /usr/lib/ruby/1.8/rexml/entity.rb   2008-10-17 21:18:59.731379482 +0900
@@ -73,7 +73,7 @@
# all entities -- both %ent; and &ent; entities.  This differs 
from
# +value()+ in that +value+ only replaces %ent; entities.
def unnormalized
-   document.record_entity_expansion
+   document.record_entity_expansion unless document.nil?
v = value()
return nil if v.nil?
@unnormalized = Text::unnormalize(v, parent)


The same patch for ruby1.8 source package is:

--- debian/patches/168_rexml_dos.patch.ORIG 2008-10-17 20:56:29.0 
+0900
+++ debian/patches/168_rexml_dos.patch  2008-10-17 21:16:53.330108500 +0900
@@ -44,7 +44,7 @@
# all entities -- both %ent; and &ent; entities.  This differs 
from
# +value()+ in that +value+ only replaces %ent; entities.
def unnormalized
-+  document.record_entity_expansion
++  document.record_entity_expansion unless document.nil?
v = value()
return nil if v.nil?
@unnormalized = Text::unnormalize(v, parent)


Thank you.

-- System Information:
Debian Release: 4.0
  APT prefers stable
  APT policy: (500, 'stable')
Architecture: amd64 (x86_64)
Shell:  /bin/sh linked to /bin/bash
Kernel: Linux 2.6.25
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)

Versions of packages libruby1.8 depends on:
ii  libc6  2.3.6.ds1-13etch7 GNU C Library: Shared libraries
ii  libncurses55.5-5 Shared libraries for terminal hand
ii  zlib1g 1:1.2.3-13compression library - runtime

libruby1.8 recommends no packages.

-- debconf-show failed



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