#! /usr/bin/env guile
!#

(use-modules (srfi srfi-1)
             (srfi srfi-26)
             (rnrs bytevectors)
             (ice-9 getopt-long)
             (ice-9 match)
             (ice-9 regex)
             (transform strings)
             (transform sql)
             (transform triples)
             (transform special-forms))



(define (remap-species-identifiers str)
  "This procedure remaps identifiers to standard binominal. Obviously this should
   be sorted by correcting the database!"
  (match str
    ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
    ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
    ["Macaca mulatta" "Macaca nemestrina"]
    ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
    [str str]))

(define-transformer genbank
  (tables (Genbank
           (left-join Species "USING (SpeciesId)")))
  (schema-triples
   (gnc:nucleotide a skos:Concept)
   (gnt:hasSequence rdfs:domain gnc:nucleotide))
  (triples (ontology
            'genbank:
            (field Genbank Id))
    (set gnt:hasSequence (field Genbank Sequence))
    (set gnt:belongsToSpecies
         (string->identifier "" (remap-species-identifiers (field Species Fullname))
                             #:separator ""
                             #:proc string-capitalize-first))))



(let* ((option-spec
        '((settings (single-char #\s) (value #t))
          (output (single-char #\o) (value #t))
          (documentation (single-char #\d) (value #t))))
       (options (getopt-long (command-line) option-spec))
       (settings (option-ref options 'settings #f))
       (output (option-ref options 'output #f))
       (documentation (option-ref options 'documentation #f))
       (%connection-settings
        (call-with-input-file settings
          read)))

  (with-documentation
   (name "Genebank Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
      ("gn:" "<http://genenetwork.org/id/>")
      ("gnc:" "<http://genenetwork.org/category/>")
      ("gnt:" "<http://genenetwork.org/term/>")
      ("dct:" "<http://purl.org/dc/terms/>")
      ("foaf:" "<http://xmlns.com/foaf/0.1/>")
      ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
      ("ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>")
      ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
      ("genbank:" "<https://bioregistry.io/reference/genbank:>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")))
   (inputs
    (list
     genbank))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))