#! /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 gn:platform->metadata
  (tables (GeneChip
           (left-join Species "USING (SpeciesId)")))
  (schema-triples
   (gnc:gene_chip a skos:ConceptScheme)
   (gnc:gene_chip skos:prefLabel "Gene Chip Vocabulary")
   (gnc:gene_chip skos:definition "A controlled vocabulary used to describe gene chip and microarray platforms.")
   (gnt:has_geo_series_id rdf:type owl:ObjectProperty)
   (gnt:has_geo_series_id rdf:label "has GEO Series ID")
   (gnt:has_geo_series_id rdfs:domain skos:Concept)
   (gnt:has_go_tree_value a owl:ObjectProperty)
   (gnt:has_go_tree_value rdfs:label "has GO tree value")
   (gnt:has_go_tree_value
    rdfs:comment
    "Associates a gene chip concept with a Gene Ontology term used for categorization.")
   (gnt:has_go_tree_value rdfs:domain skos:Concept)
   (gnt:has_go_tree_value rdfs:range xsd:string))
  (triples (string->identifier "platform" (field GeneChip Name) #:separator "_")
    (set rdf:type 'skos:Concept)
    (set skos:inScheme (field GeneChip GeneChipName))
    (set skos:prefLabel (field GeneChip Name))
    (set skos:altLabel (field ("IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL)"
                               Title)))
    (set gnt:has_go_tree_value (field GeneChip Go_tree_value))
    (set gnt:has_species
         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
    (set gnt:has_geo_series_id
         (ontology 'geoSeries:
                   (string-trim-both (field GeneChip GeoPlatform))))))



(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 "GeneChip Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
      ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
   (inputs
    (list gene-chip))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))