Add nucleotideSequence filter support to occ_download

[jhnwllr]

Background

PR #851 successfully added support for all 13 nucleotideSequence.* filter parameters to occ_search() and occ_count() functions. However, occ_download() uses a different mechanism (predicate-based downloads via the GBIF download API) and does not yet support these filters.

Current Status

✅ Supported in:

• occ_search() - uses GET /occurrence/search
• occ_count() - wraps occ_search()

❌ Not yet supported in:

• occ_download() - uses POST /occurrence/download/request with predicate JSON

Requested Feature

Add support for the following nucleotideSequence filters in the download predicate DSL:

1. nucleotideSequence.nucleotideSequenceID (string)
2. nucleotideSequence.targetGene (string) - vocabulary reference
3. nucleotideSequence.sequence (string)
4. nucleotideSequence.sequenceLength (numeric/range)
5. nucleotideSequence.gcContent (numeric/range)
6. nucleotideSequence.nonIupacFraction (numeric/range)
7. nucleotideSequence.nonACGTNFraction (numeric/range)
8. nucleotideSequence.nFraction (numeric/range)
9. nucleotideSequence.nRunsCapped (numeric/range)
10. nucleotideSequence.naturalLanguageDetected (boolean)
11. nucleotideSequence.endsTrimmed (boolean)
12. nucleotideSequence.gapsOrWhitespaceRemoved (boolean)
13. nucleotideSequence.invalid (boolean)
14. isSequenced (boolean)

Implementation Requirements

1. Predicate DSL Updates (R/download_predicate_dsl.r):

   • Add nucleotideSequence parameters to allowed predicate keys
   • Ensure proper handling of dot notation in parameter names
   • Support appropriate operators for each parameter type (equals, range, boolean)

2. Examples:

# Download all ITS1 sequences
occ_download(pred("nucleotideSequence.targetGene", "ITS1"))

# Download sequences with specific GC content range
occ_download(
  pred("nucleotideSequence.targetGene", "COI"),
  pred_gte("nucleotideSequence.gcContent", 0.4),
  pred_lte("nucleotideSequence.gcContent", 0.6)
)

# Download valid sequences only
occ_download(pred("nucleotideSequence.invalid", FALSE))

# Complex query combining taxonomy and sequence filters
occ_download(
  pred("taxonKey", 212),  # Aves
  pred("nucleotideSequence.targetGene", "COI"),
  pred_gte("nucleotideSequence.sequenceLength", 500),
  pred("nucleotideSequence.invalid", FALSE)
)

[jhnwllr]

These search parameters are not yet supported.