#! /usr/bin/env guile
!#

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



(define-transformer gn-genewiki-entries
  (tables (GeneRIF
           (left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId")
           (left-join GeneRIFXRef "ON GeneRIFXRef.GeneRIFId = GeneRIF.Id")
           (left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id"))
          "WHERE GeneRIF.display > 0 AND GeneRIF.comment IS NOT NULL
GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol")
  (schema-triples
   (gnc:GeneWikiEntry a rdfs:Class)
   (gnc:GNWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
   (gnt:initial a owl:ObjectProperty)
   (gnt:initial rdfs:domain gnc:GeneWikiEntry)
   (gnt:initial skos:definition "Optional user or project code or your initials")
   (gnt:reason a owl:ObjectProperty)
   (gnt:reason rdfs:domain gnc:GeneWikiEntry)
   (gnt:reason skos:definition "The reason why this resource was modified")
   (gnc:GNWikiEntry rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork")
   (gnt:geneSymbol rdfs:domain gnc:GNWikiEntry))
  ;; We want to avoid manually generating a unique identifier for each
  ;; comment.  As such we use a blank node (that has the comment) as
  ;; the subject of the triples produced by matching the
  ;; predicateObjectList production:
  ;; <https://www.w3.org/TR/turtle/#grammar-production-predicateObjectList>
  (triples
      (format #f "[ rdfs:label '''~a'''@en] "
              (field GeneRIF comment))
    (set rdf:type
         (let* ((create-time (field
                              ("CAST(createtime AS CHAR)" EntryCreateTime)))
                (pmid (field GeneRIF PubMed_ID PMID))
                (web-url (field GeneRIF weburl))
                (species (string->identifier
                          ""
                          (remap-species-identifiers (field Species Fullname))
                          #:separator ""
                          #:proc string-capitalize-first))
                (version-id (field GeneRIF versionId))
                (identifier (field GeneRIF Id))
                (initial (sanitize-rdf-string (field GeneRIF initial)))
                (reason (field GeneRIF reason))
                (email (sanitize-rdf-string (field GeneRIF email)))
                (category
                 (field ("GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR ';')"
                         GeneCategory))))
           (string->symbol
            (string-append
             (format #f "gnc:GNWikiEntry ;\n")
             (if (string? species)
                 ""
                 (format #f "\tgnt:belongsToSpecies ~a ;\n"
                         species))
             (format #f "\tdct:created ~s^^xsd:datetime ;\n"
                     create-time)
             (if (and (string? pmid) (not (string-null? pmid)))
                 (format #f
                         "\tdct:references ( ~{pubmed:~a ~}) ;\n"
                         (string-split pmid #\space))
                 "\tdct:references rdf:nil ;\n")
             (if (string-blank? email)
                 ""
                 (format #f "\tfoaf:mbox <~a> ;\n" email))
             (format #f "\tdct:identifier \"~s\"^^xsd:integer ;\n" identifier)
             (if (and (string? web-url) (not (string-null? web-url)))
                 (format #f "\tfoaf:homepage <~a> ;\n"
                         web-url)
                 "")
             (format #f "\tdct:hasVersion \"~s\"^^xsd:integer ;\n" version-id)
             (if (or (null? initial)
                     (string-blank? initial))
                 "" (format #f "\tgnt:initial ~s ;\n" initial))
             (if (string-blank? reason)
                 ""
                 (format #f "\tgnt:reason ~s ;\n" reason))
             (if (string-blank? category)
                 "\tgnt:belongsToCategory rdf:nil ;\n"
                 (format #f
                         "\tgnt:belongsToCategory ( ~{~s ~}) ;\n"
                         (string-split category #\;)))
             ;; We have this symbol at the very end of this transform
             ;; because we have a strong guarantee that it will be a
             ;; non-null value hence always terminating this triple
             ;; properly with a "."
             (format
              #f "\tgnt:symbol ~a"
              (string->identifier
               "symbol"
               (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                         (field GeneRIF symbol)
                                         'pre "_" 'post)
               #:proc (lambda (x) x)))))))))

(define-transformer ncbi-genewiki-entries
  (tables (GeneRIF_BASIC
           (left-join Species "USING (SpeciesId)"))
          "WHERE GeneRIF_BASIC.comment IS NOT NULL AND TRIM(GeneRIF_BASIC.comment) != '' AND TRIM(GeneRIF_BASIC.symbol) != '' GROUP BY GeneRIF_BASIC.comment, GeneRIF_BASIC.createtime, GeneRIF_BASIC.VersionId, GeneRIF_BASIC.SpeciesId, GeneRIF_BASIC.TaxID")
  (schema-triples
   (gnc:NCBIWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
   (gnc:NCBIWikiEntry rdfs:comment "Represents GeneRIF Entries obtained from NCBI")
   (gnt:hasVersionId a owl:ObjectProperty)
   (gnt:hasVersionId rdfs:domain gnc:NCBIWikiEntry)
   (gnt:hasVersionId skos:definition "The VersionId of this this resource"))
  (triples
      (string->identifier
       "symbol"
       (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                 (field GeneRIF_BASIC symbol GeneRIFSymbol)
                                 'pre "_" 'post)
       #:proc (lambda (x) x))
    (set rdfs:comment
         (let ([ncbi-comment (sanitize-rdf-string (field GeneRIF_BASIC comment))]
               [species-name
                (string->identifier
                 ""
                 (remap-species-identifiers (field Species Fullname SpeciesFullName))
                 #:separator ""
                 #:proc string-capitalize-first)]
               [taxonomic-id (field GeneRIF_BASIC TaxID TaxonomicId)]
               [create-time (field GeneRIF_BASIC createtime EntryCreateTime)]
               [pmid (field GeneRIF_BASIC PubMed_ID PMID)]
               [gene-id (field GeneRIF_BASIC GeneId)]
               [version-id (field GeneRIF_BASIC VersionId)])
           (string->symbol
            (string-append
             "[ "
             (format #f "rdf:type gnc:NCBIWikiEntry ; ")
             (format #f "rdfs:comment ~s^^xsd:string ; "
                     ncbi-comment)
             (format #f "gnt:belongsToSpecies ~a ; "
                     species-name)
             (if (eq? #f taxonomic-id)
                 ""
                 (format #f "skos:notation taxon:~a ; "
                         taxonomic-id))
             (format #f "gnt:hasGeneId generif:~a ; "
                     gene-id)
             (format #f "dct:hasVersion '~a'^^xsd:int ; "
                     version-id)
             (if (and (string? pmid) (not (string-null? pmid)))
                 (format #f
                         "~{dct:references pubmed:~a ; ~}"
                         (string-split pmid #\space))
                 "")
             (if (string? create-time)
                 ""
                 (format #f "dct:created ~s^^xsd:datetime ; "
                         (time-unix->string
                          create-time "~5")))
             " ]"))))))



(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 "GeneRIF 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/>")
      ("taxon:" "<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#>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")))
   (inputs
    (list
     gn-genewiki-entries
     ncbi-genewiki-entries))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))