Reporting Issues

[charvolant]

Issues for ag-bie reporting. These may be addressed in other components but this is a good place to park things.

• [x] Raw input count
• [x] Count of discarded taxa for whatever reason. (This should not be happening)
• [x] Turn count.load.VIRUS and friends into count.load.nametype.VIRUS to make it clear this isn't coming from the kingdom.
• [x] Turn count.resolve.taxonConcept should be taxon concept instances to taxon concepts
• [x] Include code, rank, dataset, taxonomic status in report
• [ ] When choosing first in collisions, the chosen taxon should appear in the taxonID column
• [x] *.collision.match should be more clear about it just choosing the first (collision.warn)
• [ ] Include a log of names that have been simply, incontestably allocated.
• [x] Scientific name authorship, ensure it's in the report
• [ ] Subfamily mapped onto family
• [ ] "Removing placeholder ..." is a bad message since it only get removed at the end. Include action.

[ess-acppo-djd]

Note:

Include a log of names that have been simply, incontestably allocated.

Don't log each name in the report, just include a count.

[ess-acppo-djd]

Specifically regarding the NAQS BioLink taxon input (tblBiota)

Names defined in the input as Literature Names (bitLiteratureName = 1) or Available Names (bitAvailableName = 1) are to be treated as synonyms of their parent record.

As synonyms of their parent, they should be treated as having a principal taxon which is their parent record, which is the accepted name for which they are a synonym.

Currently, these records trigger a diagnostic of

dcterms:type=NOTE 
dcterms:subject=taxonResolver.noPrincipals
dcterms:description="Taxon TC[taxon concept details] has no principals, using all instances"

It is preferable this be suppressed for any name explicitly identified as a synonym.

[charvolant]

Stuff done so far.

• Raw input count
  • Appears as count.load.instance
• Count of discarded taxa for whatever reason. (This should not be happening)
  • Appears as count.load.forbidden
• Turn count.load.VIRUS and friends into count.load.nametype.VIRUS to make it clear this isn't coming from the kingdom.
  • Turned into count.load.name.VIRUS
• Turn count.resolve.taxonConcept should be taxon concept instances to taxon concepts
  • count.resolve.taxonConceptInstance counts the number of taxon concept instances that have been resolved. count.resolve.taxonConcept is the number of taxon concepts that have been resolved.
• Include code, rank, dataset, taxonomic status in report
  • Added When choosing first in collisions, the chosen taxon should appear in the taxonID column
  • Done
• *.collision.match should be more clear about it just choosing the first (collision.warn)
  • Done and reamed to collision.warn
• Scientific name authorship, ensure it's in the report
  • Fixed

[moziauddin]

Reporting issues are now resolved.