[Gmod-apollo-cmts] CVS: apollo/doc das2-todo,1.2,1.3

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Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25192

Modified Files:
	das2-todo 
Log Message:


Index: das2-todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/das2-todo,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** das2-todo	14 Feb 2006 22:28:09 -0000	1.2
--- das2-todo	22 Mar 2006 23:48:33 -0000	1.3
***************
*** 1,26 ****
  DAS2 adapter gui:
! x If you open the adapter first to write DAS2 and then do "load data", it
! opens showing the writer GUI, not the reader.  (Same problem if you do
! "load" first and then "save as"--it doesn't redo the GUI.)
  - Don't enable OK button until user has filled in acceptable start/end.
! Check end against segment end and requested length against max length.
! - Why is it so slow?
! - "Previous selections" pulldown shows boring part of URL--can't see
! actual range.
! x Redundant items being added to history list and server list [This may
! have been due to a screwed-up history]
  - When you ask to save a das2xml file, the label should say "DAS2XML file",
  not "DAS/2 server".
  
  Get sources/segments/types
! - Get list of servers from registry
! - Get DAS/2 version info from header
! x Segment query was using canned response when Allen's server had a
! bug--return to real request
! - Extension to query to get desired document (e.g. "/features") shouldn't
! be hardcoded--need to get from CAPABILITY element in SOURCES document:
!       <CAPABILITY type="features" query_id="volvox/1/features">
! this could equally well say
!       <CAPABILITY type="features" query_id="volvox/1/pineapple">
  - Not yet getting list of types from server--for now, we're just getting
  all types in requested region.  Need type chooser GUI (like in ensembl
--- 1,49 ----
+ Sample region to try:
+ http://das.biopackages.net/das/genome/yeast/S228C/segment
+ chrVII
+ 364999-366100
+ URL: http://das.biopackages.net/das/genome/yeast/S228C/feature?overlaps=chrVII/364999:366100
+ 
+ Apollo's DAS/2 adapter is now (roughly) compatible with DAS/2 version 300
+ (3/172006).
+ 
  DAS2 adapter gui:
! - Sanity-check requested region.  Check end against segment end and
! requested length against max length.  [The latter is done.  It would
! be nice, in the future, if we could send a "how many elements in this
! region?" query before deciding whether the requested range is reasonable.]
  - Don't enable OK button until user has filled in acceptable start/end.
! - Redundant items being added to history list and server list (I thought
! this was fixed but it's still happening).
  - When you ask to save a das2xml file, the label should say "DAS2XML file",
  not "DAS/2 server".
+ x "Previous selections" history pulldown shows boring part of
+ URL--can't see actual range.  (It seems to show two URLs--the server
+ URL and then the URL for the specific range.  The server URL can be
+ seen, but the one for the range is cut off.  Can we just display the
+ second URL in that list, and leave off the first?)
+ [Improved somewhat by listing the versioned source first, then the
+ segment (chromosome), then the start/end, and the main server URL
+ last (where user can't see it.]
+ - History: I thought this wouldn't work if we didn't explicitly save
+ the capabilities in that big ugly string, but it seems to work
+ fine--maybe we can leave some of that other stuff out as well??
+ - Sometimes there are duplicate items in history
+ 
+ Things to get from header:
+ - xml:base
+ - DAS/2 version number (Apollo should complain if this number is
+ higher than what it knows about).
+ If version is >300 (which is the version of March 2006), Apollo should
+ pop up a warning message saying it doesn't know how to deal with data of
+ that version.
+ To see header:
+ GET -e "http://das.biopackages.net/das/genome/yeast/S228C/feature?overlaps=chrI/1:222"
+ Header includes a line like:
+ Content-Type: application/x-das-features+xml; version=300
  
  Get sources/segments/types
! - Get list of versioned sources from registry [registry wasn't working on
! 3/16/2006] "http://www.spice-3d.org/dasregistry/das2/sources/"
  - Not yet getting list of types from server--for now, we're just getting
  all types in requested region.  Need type chooser GUI (like in ensembl
***************
*** 29,32 ****
--- 52,56 ----
  - Enable navigation bar on main window
  - Get sequence--not implemented yet
+ - Get display style for type
  
  Feature parser:
***************
*** 38,39 ****
--- 62,79 ----
  results if we read from a DAS2XML file and thus don't have region info.
  ("Set region to segment/chrVII:327945-365258 + 4 based on extent of first and last results")
+ 
+ Need to update DAS2XML writer--not even fully 200-compliant, let alone 300.
+ 
+ Clean up
+ - Pretty much everything.  Lots of legacy code from the DAS/1 adapter
+ needs to be cleared out.
+ ----------------------------------------------------------------------------
+ Fixed recently
+ x If you open the adapter first to write DAS2 and then do "load data", it
+ opens showing the writer GUI, not the reader.  (Same problem if you do
+ "load" first and then "save as"--it doesn't redo the GUI.)
+ x Extension to query to get desired document (e.g. "/features") shouldn't
+ be hardcoded--need to get from CAPABILITY element in SOURCES document:
+       <CAPABILITY type="features" query_id="volvox/1/features">
+ this could equally well say
+       <CAPABILITY type="features" query_id="volvox/1/pineapple">