#! /usr/bin/env guile
!#

(use-modules (rnrs programs)
             (rnrs io ports)
             (srfi srfi-1)
             (srfi srfi-26)
             (ice-9 getopt-long)
             (ice-9 match)
             (ice-9 regex)
             (transform strings)
             (transform sql)
             (transform triples)
             (transform special-forms))

(define-transformer gn:markers/snps->metadata
  (tables (Geno
           (inner-join Species "ON Geno.SpeciesId = Species.Id"))
          "WHERE Species.Name != 'monkey'")
  (triples (string->identifier "marker" (field Geno Name) #:separator "_")
    (set gnt:has_species
         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
    (set rdf:type 'gnc:dna_marker)
    (set skos:prefLabel (field Geno Name))
    (set skos:altLabel (field Geno Marker_Name))
    (set gnt:chr (field Geno Chr))
    (set gnt:mb (annotate-field (field Geno Mb) '^^xsd:doubleg))
    (set gnt:sequence (field Geno Sequence))
    (set gnt:source (field Geno Source))
    (set rdfs:comment (field Geno Comments))))



(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 "Phenotypes Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("dcat:" "<http://www.w3.org/ns/dcat#>")
      ("dct:" "<http://purl.org/dc/terms/>")
      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
      ("gnd:" "<https://cd.genenetwork.org/lmdb/v1/data/traits/>")
      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
      ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
      ("qb:" "<http://purl.org/linked-data/cube#>")
      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
      ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
   (inputs
    (list gn:markers/snps->metadata))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))