[DAS] 1.0 spec questions

[Lincoln Stein]

Hi Andrew,

The stylesheet spec has been allowed to languish.  Thanks for picking up the 
inconsistencies between the written spec and the DTD, and I'll get them fixed 
ASAP.

As far as the regression tests go, there are regression tests for the 
Bio::Das Perl client side library, which you'll find in the t/ subdirectory.  
Since Thomas has started picking up errors in the LDAS server, I'll be 
putting in regression tests for the server as well soon.

Lincoln

On Saturday 02 February 2002 03:54, Andrew Dalke wrote:
> Hi,
>
> Let me start by saying that I haven't looked at DAS in a while
> nor have I followed the list.  I searched the list for my
> questions but didn't find anything appropriate.
>
> So I'm starting to get a feel for DAS at the data interchange
> level.  I'm using a DTD to Python class generator called 'PAXB'
> (it's based on JAXB but is 0.1 code and it shows).  It looks
> like there are differences between
>
> http://www.biodas.org/dtd/dasstyle.dtd
>   and
> http://www.biodas.org/documents/sample_stylesheet.xml
>   and the 1.0 spec at
> http://biodas.org/documents/spec.html
>
> These are still present in the CVS files.
>
> Here's the differences I found so far.
>
> That XML file is not well-formed -
>
> * End tag 'BOXS' does not match the start tag 'BOX'. Line 166, Position 13
>
> Here's the relevant XML
>           <BOX>
>             <HEIGHT>3</HEIGHT>
>             <FGCOLOR>black</FGCOLOR>
>             <LABEL>yes</LABEL>
>             <BGCOLOR>red</BGCOLOR>
>             <BUMP>yes</BUMP>
>           </BOXS>
>           ^^^^^^^ should be 'BOX'
>
> The DTD needs to have "WIDTH" changed to "HEIGHT" (according to
> Version 0.99 changelog info)
>
> The DTD doesn't include the "FGCOLOR" nor "BGCOLOR" definitions.
>
> In the DTD, LINE needs to include a "STYLE" and a "LINEWIDTH",
> which are used in the XML file.
>
> The DTD is missing ANCHORED_ARROW, which is in the XML file
> and in the spec.  (I see that Brian's XMLSPY output at
>
> http://www-genome.wi.mit.edu/personal/gilmanb/i3c/xmlspy_docs/das/style.htm
>l also doesn't have ANCHORED_ARROW nor does any of the code in the
> CVS release.)
>
> The spec has a "HIDDEN" glyph which is not in the DTD nor is
> in the XML.  (Added in Version 1.0)
>
> The XML file has LINEWIDTH for ANCHORED_ARROW, which probably
> implies ARROW needs it as well in the DTD.
>
> The XML file has "POINT"s for TRIANGLE and BOX, but there is
> no POINT in the XML.  Nor is there a "POINT" in the spec.
>
> The DTD defines a "CONNECTOR" which is not listed in the spec.
>
> What's the interpretation of "PRIMERS"?
>
>         <GLYPH>
>           <PRIMERS>
>             <HEIGHT>50</HEIGHT>
>             <FGCOLOR>#33ff33</FGCOLOR>
>             <LABEL>yes</LABEL>
>           </PRIMERS>
>         </GLYPH>
>
> What's the interpretation of "SEGMENTS"?
>         <GLYPH>
>           <SEGMENTS>
>             <HEIGHT>50</HEIGHT>
>             <FGCOLOR>#666666</FGCOLOR>
>             <LABEL>yes</LABEL>
>             <LINEWIDTH>1</LINEWIDTH>
>           </SEGMENTS>
>         </GLYPH>
>
> And 'TRANSCRIPT'?  Shouldn't all three of these be stored
> as a TYPE id?
>
> There's still a 'FILLCOLOR' in sample_stylesheets.xml .
> I believe this should be 'BGCOLOR'
>
> Line 571 of that file needs a /CATEGORY as otherwise the
> document is not well formed.  Eg, see the comment in the
> following grep
>
> cvs:documents {410} grep CATEGORY sample_stylesheet.xml
>   <CATEGORY id="group">
>   </CATEGORY>
>   <CATEGORY id="structural">
>     </CATEGORY>
>     <CATEGORY id="similarity">
>     </CATEGORY>
>     <CATEGORY id="variation">
>     </CATEGORY>
>     <CATEGORY id="experimental">
>     </CATEGORY>
>     <CATEGORY id="translation">  *--- Where's the close?
>     <CATEGORY id="transcription">
>     </CATEGORY>
>     <CATEGORY id="repeat">
>     </CATEGORY>
>     <CATEGORY id="default">
>     </CATEGORY>
> cvs:documents {411}
>
> Am I working off of outdated documents?  Or is the DTD really
> incomplete?
>
>
> I also did a quick scan of the geodesic code to see what it
> handles.  I see that:
>  - "CONNECTOR" is not on the spec page
>  - it doesn't support "ANCHORED_ARROW"
>  - it doesn't support "HIDDEN"
>  - it has "OUTLINECOLOR" instead of "BGCOLOR"
> I did not to a full search so may have missed things.
>
> Also, where are the regression tests?  I wanted to see how
> easy it is to use them from Python.
>
>                     Andrew Dalke
>                     dalke@dalkescientific.com
>
>
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================