* Search generally

** Implement new interface as per Bill's mockup

** Minor user interface matters

*** [#A] Uniform table headings between summary and search results pages.  Share code?
*** [#A] trees.html" has a spurious "1" above the table

*** Tighten up search results page
**** [#A] Combine author name and study text search  boxes

*** Clean up Bill-Val notes as necessary
    20081002 Hidden, but still present.  
    20081016 Deleted several; ongoing

*** Move "See all trees/matrices" buttons to bottom of page

** Report misspellings in tree topology searches

** Tree searches
*** Tree search by Tree ID

** Matrix searches
*** Matrix text searches
**** Character names
**** Character state names
**** Character set names
**** Search for single taxon
**** Matrix title
*** Matrix type searches (sequence, dna, etc.)

** Specify page length in search results 

BP 20080725 <894B7889-B95D-4578-8ADD-9F045C23D3EC@yale.edu>

** Clicking column heads to sort results doesn't work
*** 20081010 It worked in at least some instances

* Taxonomic intelligence in search

PREREQUISITE: repatriate taxonlabel information

** Design new search / diambiguation JSP components

** Programming for new search / diambiguation JSP components

* Display

** PhyloWidget display changes

As per <894B7889-B95D-4578-8ADD-9F045C23D3EC@yale.edu> 20080725

** Implement matrix / tree "download" links
*** Also add them to matrix.jsp

** Adjustable amount of data in matrix row view

Tough; confer with Jin on this

** Row segment display
*** "Not implemented" header misformatted

* Data importation

** Resolve symbolstring / elementstring confusion
*** Missing element character states?

** Import remaining matrices
*** What about the missing 200 matrices?

** Merge remaining matrix/tree/analysis information
*** Studies by Goldblatt: why no matrices 20080825?

** Separate citation information into title, summary, etc.
*** Write Perl thingy for DB data
**** Fix author order and author names
**** Fix author first / middle names
**** Publication dates
*** Apply Rod Page's bibliographic information
**** Mapping of studies to pubMed identifiers
**** Journal name linking in TB1 data as per BP email

** Merge duplicate taxon labels in each study
*** Regenerate taxonlabelsets

** [#A] Fix tree-treeblock associations

** Import taxonLabel -> taxonVariant -> taxon data
*** Study 7221 taxa not properly linked 20080825

** Copy TB_STUDYID to ACCESSIONNUMBER to that the former can be destroyed

** Garbage collection: destroy unused objects
*** [#A] Delete dummy studies and submissions
**** Why is deleteStudy so slow?  Takes 28 minutes per study!

** [#A] Find and delete obvious test studies

* Documentation

** Design document for parsing system

** How to get detailed DB2 error diagnostics in a Java exception dump?

Experiment with querying nested exceptions

20081013 ongoing; see util/DBETest.java 

* Bugs

** Study taxon search for "Patu" + "Canis familiaris" did something weird

I forget what, but it must have been obviously wrong.

** Tree #2128 fails with PhyloWidget
** Topology searches fail when fed misspelled taxon names
** Taxon search with empty box fails
*** Write tests for these

** "Search among these results" didn't work for a tree taxon search with "OR"
** Tree taxon search for "Bos taurus" returned no results.  Why?

** Weird error when converting trees to studies; Val sent backtrace

** RHS menu generally screwed up.  Get Madhu to help.  
*** Propagate Rutger's fix to all pages.

*** On Tree search page, it's at the bottom instead of on the right.  Why?

** Null form name will cause NPE in SearchController derived classes

* Performance

* Internal matters

** Idea: search results structure change

Instead of encapsulating one set of search results, the search results
object can be a lazily-populated study + matrix + tree set.
Modifying one set will invalidate the other two portions.
Then the buttons can be predicated on the emptiness of the corresponding
portion.

** Build dumper based on direct Perl queries to DB

This will save a lot of SQL writing at the command line when something
is wrong.

* Help system

* Other

** Remind Val to thank Rod Page for citation parsing etc.
** use schemaSpy to build remaining ER diagrams.  Check in.

** Bill Piel requests of 20080808
*** Merge these into TODO lists

** Make sure you have access to FogBugz