#! /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:genotype->metadata
  (tables (InbredSet
           (inner-join GenoFreeze "ON GenoFreeze.InbredSetId = InbredSet.Id")
           (inner-join InfoFiles "ON InfoFiles.InbredSetId = InbredSet.Id"))
          "WHERE GenoFreeze.public > 0 GROUP BY GenoFreeze.Id")
  (schema-triples
   (gnc:genotype a owl:Class)
   (gnc:genotype a skos:Concept)
   (gnc:genotype rdfs:label "A genotype."))
  (triples (string->identifier "genotype" (field GenoFreeze Name) #:separator "_")
    (set rdf:type 'gnc:genotype)
    (set skos:prefLabel (field GenoFreeze FullName))
    (set skos:altLabel (field GenoFreeze ShortName))
    (set dct:created (annotate-field (field GenoFreeze CreateTime) '^^xsd:datetime))))


(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 "Genotype Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("dct:" "<http://purl.org/dc/terms/>")
      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
   (inputs
    (list gn:genotype->metadata))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))