[DAS] PyDAS-0.8, including validation suite

[Andrew Dalke]

I've made PyDAS-0.8 available (temporarily) at
 http://www.biopython.org/~dalke/PyDAS-0.8.tar.gz

Included in the distribution is a validation suite called
'dascheck' which I wrote because of the various problems
I found in the different servers.  dascheck requires you also
download and install the PyXML package from
  http://pyxml.sourceforge.net/
  

For example, here's the summary section of after run
against the latest LDAS server.  (I've been forwarding this
to Lincoln as I found them.)

Summary of results
WARNING: Incorrect DAS-VERSION header 'DAS/1.50', expected 'DAS/1.5'
WARNING: Server says stylesheet for DSN 'elegans' does not exist
WARNING: entry_point returns both 'size' and start/stop attributes
ERROR: Invalid XML: the document starts with '<?xml version="1.0" standalone="yes"?' -- missing the '>' after the last '?'
ERROR: Command 'sequence' not supported
ERROR: Returned XML in <dsn>/types request does not match the DTD: invalid attribute name ('summary') for this element ('GFF')
WARNING: The permissive parser was needed to read <dsn>/types
WARNING: <dsn>/types returns GFF version number '1.2', expected '1.0'
WARNING: <dsn>/types returns GFF with 'summary' attribute but that is not allowed by the spec
ERROR: segment id in 'types' call must contain 'version' attribute
WARNING: DSN 'types' contains unexpected 'href' field
ERROR: Invalid XML in the <GROUP>'s id attribute
WARNING: <dsn>/features returns GFF version number '1.01', expected '1.0'
WARNING: <dsn>/features GFF contains unexpected 'href' attribute
WARNING: Server says stylesheet for DSN 'freeman' does not exist
ERROR: returned dna length differs from request
ERROR: Could not call DSN test stylesheet: 500: Internal server error
ERROR: Could not call DSN test entry_points: 500: Internal server error
ERROR: Could not call DSN test types: 500: Internal server error
ERROR: Skipping other 'types' tests


The full output goes into extreme detail, especially when used with the
  --show-urls and '--save-dir <dirname>' options.  The first shows
the POST used as a GET url and the second saves all returned XML in the
named directory (or stdout if dirname is '-').



To run 'dascheck' in its simplest form:
  - uncompress/untar it
  - cd PyDAS-0.8
  - setenv PYTHONPATH $PWD
     (or the equivalent for bash shells)
  - cd bin
  - python dascheck http://...../dsn

If you run with "--help" you get the command-line parameters.

					Andrew
					dalke@dalkescientific.com