* Search generally


** Minor user interface matters
*** Widen taxon list search box to 30 chars
*** trees.html has no "back" link

*** Tighten up search results page
**** Combine taxon set search and "see trees/matrices" and "discard results" boxes

*** "Search again" should change 
     to say "Your search has yielded 1234 studies, listed below.
     You can discard these results or you can search again among these."


*** Side menu with tabs for tree, study, matrix search
*** [#A] Get "convert" buttons pack onto search pages

*** Empty result suppression:

**** If the result set contains no trees, suppress the "see trees" button
**** If the result set contains no matrices, suppress the "see matrices" button
**** If the result set contains no studies, suppress the "see studies" button

*** "Name" column header -> "Study Name"
    Displays what for TB1 data?
*** Remove "Citation" column

*** Study summary page should include study name

** Tree searches
*** Tree taxon list / single taxon search

** Matrix searches
**** Taxon list

** Search for studies by TB1 ID
   PREREQUISITE: Jin should ad TB1_STUDYID to data model
     Done
   COREQUISITE: Rewrite TB1 methods to use data model
     Done

as per <B82EEA7B-87C9-4B02-AF49-6D40805482C3@cis.upenn.edu>

** "Discard" button fails to return user to the right place

** "Search in abstract" throws an exception

* Taxonomic intelligence in search
** Revise project plan

** new TaxonService functions

And compositions of these:

*** findTaxonVariantBySubstring
*** findTaxonByTaxonVariant
*** findAnalyzedDataByTaxon

** Incorporate taxon search into existing controllers
*** Taxon list search
*** Topology search
**** Fix incredibly weird topology-ignoring bug

** Fix broken right-hand-side menus

* Data importation
** Repatriation: link up orphan data
*** Authors
*** Taxa
*** Trees
*** Matrices

** Merge duplicate taxon labels in each study
*** Repatriate each taxonlabel to the right submission
*** Merge duplicates

* Study display
** Trees list
** Taxa page

** Investigate why authors listed in wrong order?
   Because Bill's TB1 dump doesn't have them in the right order.
   Fix this when you destructure the citation data as below.

** Row segment display
** Build row segment page
*** Link matrix rows to row segment page when appropriate
*** Display specimen information

** Garbage collection: destroy unused objects
*** [#A] Delete dummy studies and submissions
**** Refit deleteStudy program to use deleteSubmission 

* Bugs

** [#B] T4A and T4S searches broken (syntax error in query)

** Weird state errors with "?action=discard" in the URL.  

It isn't removed when it should be.  

20081002 You added code to honor
action=discard only on GET requests; this may solve the problem.
Investigate.

20081013 Resolved.

** Wrong post bug

** RHS menu generally screwed up.  Get Madhu to help.  
*** Should default to expanded

** Taxon box searches doing substrings?

Taxon search for "Patu" seems to find "X. spatula" in addition to "Patu".


** Mismatched analyses?

Analyses on study summary page don't link to the correct trees and matrices.
Study 7464 has two different matrices listed: 2729 and 2802.
One listed via analysis, one not.
Similarly the tree.

** "No data" in matrix rows

Matrices 622 and 292 have "no data".  We thought this was
characteristic of morphological character matrices, but 2729 has
morph. character and *does* have data in the rows.

Ongoing; see "Resolve symbolstring / elementstring confusion".


* Performance

** Make matrix taxon searches faster
** Make tree taxon searches faster

* Documentation

** Write up the methodology you used for debugging

The taxonlabel merger problem of 20080930.  Quickly, before you
forget.

20081016 You probably missed the window in this.

* Other
** Make sure you can publish changes on 8ball
** Make sure 8ball publishing is still working