#! /usr/bin/env guile
!#

(use-modules (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 tissue
  ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
  ;; and BIRN_lex_Name are mostly NULL.
  (tables (Tissue))
  (schema-triples
   (gnc:tissue a owl:Class)
   (gnc:tissue rdfs:subClassOf obo:UBERON_0000479) ; Anatomical Entity
   (gnc:tissue rdfs:label "Tissue (GN)")
   (gnt:has_tissue rdf:type owl:ObjectProperty)
   (gnt:has_tissue rdfs:domain gnc:molecular_traits)
   (gnt:has_tissue rdfs:range gnc:tissue)
   (gnt:has_tissue rdfs:label "has tissue"))
  (triples (string->identifier "tissue" (field Tissue Short_Name)
                               #:separator "_")
    (set rdf:type 'gnc:tissue)
    (set rdfs:label (field Tissue Name))))



(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 "Tissue Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
      ("obo:" "<http://purl.obolibrary.org/obo/>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
   (inputs
    (list tissue))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))
;; http://purl.obolibrary.org/obo/UBERON_0000479