Difference between revisions of "Galaxy Tool Tips and Troubleshooting"

From Ucsbgalaxy
Jump to: navigation, search
(Created page with "== Escaped Characters == When Galaxy runs string values from the UI in a command for a tool, it first escapes some characters to protect against injection attacks. For instance,…")
 
(Escaped Characters)
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
 
== Escaped Characters ==
 
== Escaped Characters ==
When Galaxy runs string values from the UI in a command for a tool, it first escapes some characters to protect against injection attacks.
+
When Galaxy submits string values from the UI to a tool's config file, it first escapes some characters to protect against injection attacks.
  
For instance, if a user inputs the character '#' Galaxy will convert it into '__pd__' before pushing the string into the command XML tool config statement.
+
For instance, if a user inputs the character '#' Galaxy will convert it into '__pd__' before passing the string into a tool's XML config variables.
  
As of yet, this is undocumented behavior. The full list of escaped characters can be found in galaxy-dist/lib/galaxy/util/__init__.py under the name mapped_chars.
+
The full list of escaped characters can be found in galaxy-dist/lib/galaxy/util/__init__.py under the name mapped_chars.
  
 
For reference the full list as of 11/23/2011 is:
 
For reference the full list as of 11/23/2011 is:

Latest revision as of 01:26, 24 November 2011

Escaped Characters[edit]

When Galaxy submits string values from the UI to a tool's config file, it first escapes some characters to protect against injection attacks.

For instance, if a user inputs the character '#' Galaxy will convert it into '__pd__' before passing the string into a tool's XML config variables.

The full list of escaped characters can be found in galaxy-dist/lib/galaxy/util/__init__.py under the name mapped_chars.

For reference the full list as of 11/23/2011 is:

mapped_chars = { '>' :'__gt__',
                '<' :'__lt__',
                "'" :'__sq__',
                '"' :'__dq__',
                '[' :'__ob__',
                ']' :'__cb__',
                '{' :'__oc__',
                '}' :'__cc__',
                '@' : '__at__',
                '\n' : '__cn__',
                '\r' : '__cr__',
                '\t' : '__tc__',
                '#' : '__pd__'
                }