[Treebase-devel] issue 2712225: "Messages vanish prematurely during manual taxon validation"

[Rutger V. <rut...@gm...>]

Hi,

issue 2712225 is, cryptically, about the following issue:

> 2- The warning about "had multiple hits - defaulted to first hit
> **VALIDATE BY HAND**" is good, except once I try to validate one of
> them, this message disappears, so I don't know which other ones still
> need to be validated by hand. Is there a way to continue posting this
> flag each time the page is revisited?
(https://sourceforge.net/tracker/index.php?func=detail&aid=2712225&group_id=248804&atid=1126676)

As this is the first post to treebase-devel, here's some context: when
users submit any nexus file containing taxon labels (a tree file, a
matrix file, or a combination thereof), TreeBASE initially flags these
labels as not having been linked to an external taxonomy (i.e. uBio
and NCBI). The user is then expected to go the page with taxon labels,
check all labels flagged as not linked (they have a red cross mark
next to them) and hit "validate".

TreeBASE will then attempt to look up these labels in uBio - and from
there in the NCBI taxonomy. In some cases, it will turn out that a
label is a true homonym, i.e. multiple, actual taxa by that name exist
- usually a plant taxon and an animal taxon (examples: Aotus,
Abronia). TreeBASE will pick the first option of the list of homonyms
and warn the user that it did this, urging the user to check by hand
whether that choice is the right one.

Issue 2712225 complained that this warning disappears after the first
time the user viewed the validation results page. In the case of
multiple homonyms (e.g. when a nexus file contained both Aotus and
Abronia) this is problematic because now the user needs to remember
which labels (potentially from a very large list) to resolve.

In follow up discussion, Bill clarified the issue as follows:

> So here's the problem: the user does a "Validate" and gets back a list of
> "**VALIDATE BY HAND**" messages. He picks the first one to validate by
> hand, fixes that, then goes back to the list to pick the next one that
> needs validating by hand. But now the warning messages are gone, and he
> can't possibly remember which other ones still need hand validation.
> Ideally the messages would stick around until each case that requires
> special attention is dealt with -- but I can understand that we don't want
> to constantly trigger re-validation. One solution is that any label that
> has multiple mappings gets a little "M" symbol (or whatever) in a column on
> the Taxon Labels Information page -- that always gets displayed whether
> hand validation has been used or not (it's just a property of the row).
> Another solution is that when there are VALIDATE BY HAND messages, these
> get posted to a pop-up window which can stick around while the user is
> correcting each one in the main page. The third solution is for me to try
> to give sufficiently clear instructions that the user should copy/paste the
> VALIDATE BY HAND messages to a separate text document, so as to save these
> warnings until all have been fixed.

As a fix for this as of revision 6382, I have now implemented the
following: a map (keys: taxon label IDs, values: taxon label strings)
called "homonyms" is created during taxon label validation and carried
around the session. Every time a homonym is manually resolved, that
entry is deleted from the session.

This means that warning messages about unresolved homonyms on the
taxon labels screen now persist for the duration of the session - as
opposed to disappearing after the first viewing. Every time a homonym
is resolved by hand = one less nagging warning message at the top of
the taxon labels screen.

These messages do NOT persist between sessions, i.e. when a user logs
out and logs back in again, the messages are gone. The only way to fix
that would be to add a column to the taxon labels table that can
persistently flag labels as unresolved homonyms. I personally think
that that would be excessive, so I have closed the bug report. Agreed?

Rutger