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#! /usr/bin/env guile
!#

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



(define (remap-species-identifiers str)
  "This procedure remaps identifiers to standard binominal. Obviously this should
   be sorted by correcting the database!"
  (match str
    ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
    ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
    ["Macaca mulatta" "Macaca nemestrina"]
    ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
    [str str]))

(define (fix-email-id email)
  (string-delete #\space email))

(define (investigator-attributes->id first-name last-name email)
  ;; There is just one record corresponding to "Evan Williams" which
  ;; does not have an email ID. To accommodate that record, we
  ;; construct the investigator ID from not just the email ID, but
  ;; also the first and the last names. It would be preferable to just
  ;; find Evan Williams' email ID and insert it into the database.
  (string->identifier "investigator"
                      (string-join
                       (list first-name last-name (fix-email-id email))
                       "_")))



(define-transformer genewiki-symbols
  (tables (GeneRIF_BASIC
           (left-join Species "USING (SpeciesId)"))
          "GROUP BY GeneId ORDER BY BINARY symbol")
  (schema-triples
   (gnt:belongsToSpecies rdfs:domain gnc:strain)
   (gnt:belongsToSpecies rdfs:domain gnc:NCBIWikiEntry)
   (gnt:symbol rdfs:domain gnc:NCBIWikiEntry))
  (triples (ontology 'generif: (field GeneRIF_BASIC GeneId))
    (multiset gnt:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol))
                                       #\,))
    (multiset gnt:belongsToSpecies
              (string-split
               (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species))
               #\,))
    (multiset dct:relation
              (map
               (cut ontology 'ncbiTaxon: <>)
               (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
                             #\,)))))

(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")
           (left-join Investigators "ON Investigators.Email = GeneRIF.email"))
          "WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 AND GeneRIF.comment IS NOT NULL GROUP BY GeneRIF.comment, GeneRIF.createtime")
  (schema-triples
   (gnc:GeneWikiEntry a rdfs:Class)
   (gnc:GNWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
   (gnc:GNWikiEntry rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork")
   (gnt:belongsToCategory rdfs:domain gnc:GNWikiEntry)
   (gnt:belongsToSpecies rdfs:domain gnc:GNWikiEntry)
   (gnt:symbol rdfs:domain gnc:GNWikiEntry))
  (triples
    (string->identifier
     "generif"
     (make-version-3-uuid
      (u8-list->bytevector
       ;; URL namespace UUID is 6ba7b811-9dad-11d1-80b4-00c04fd430c8
       '(107 167 184 17 157 173 17 209 128 180
             0 192 79 212 48 200))
      (format #f "~a~a~a~a"
              (field Species FullName)
              (field GeneRIF comment)
              (field GeneRIF symbol)
              (field GeneRIF createtime))
      ""))
    (set rdf:type 'gnc:GNWikiEntry)
    (set rdfs:label (sanitize-rdf-string (field GeneRIF comment)))
    (set gnt:symbol (field GeneRIF symbol))
    (multiset gnt:belongsToCategory
              (remove-duplicates
               (string-split-substring
                (field ("GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR '$$')"
                        GeneCategory))
                "$$")))
    (set gnt:belongsToSpecies
         (string->identifier
          ""
          (remap-species-identifiers (field Species Fullname))
          #:separator ""
          #:proc string-capitalize-first))
    (multiset dct:references
              (map (lambda (x)
                     (ontology 'pubmed: x))
                   (string-split
                    (let ((pmid (field
                                 ("IFNULL(GeneRIF.PubMed_ID, '')"
                                  PubMed_ID))))
                      (if (number? pmid)
                          (number->string pmid)
                          pmid))
                    #\space)))
    (set dct:created
         (let ((createtime (field GeneRIF createtime)))
           (if (string? createtime)
               ""
               (annotate-field
                (time-unix->string
                 createtime "~5")
                '^^xsd:datetime))))
    (set dct:creator
         (if (and (not (string-null?
                        (string-trim-both (field GeneRIF email))))
                  (not (string-null? (field Investigators Email))))
             (investigator-attributes->id
              (field Investigators FirstName)
              (field Investigators LastName)
              (field Investigators Email))
             ""))
    (set foaf:homepage (field GeneRIF weburl))))

(define-transformer ncbi-genewiki-entries
        (tables (GeneRIF_BASIC)
                "GROUP BY GeneId, comment, createtime")
        (schema-triples
         (gnc:NCBIWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
         (gnc:NCBIWikiEntry rdfs:comment "Represents GeneRIF Entries obtained from NCBI"))
        (triples
            (string->identifier
             "generif"
             (make-version-3-uuid
              (u8-list->bytevector
               ;; URL namespace UUID is 6ba7b811-9dad-11d1-80b4-00c04fd430c8
               '(107 167 184 17 157 173 17 209 128 180
                     0 192 79 212 48 200))
              (format #f "~a~a~a~a~a"
                      (field GeneRIF_BASIC GeneId)
                      (field GeneRIF_BASIC VersionId)
                      (field GeneRIF_BASIC comment)
                      (field GeneRIF_BASIC symbol)
                      (field GeneRIF_BASIC createtime))
              ""))
          (set rdf:type 'gnc:NCBIWikiEntry)
          (set rdfs:label
               (annotate-field (field GeneRIF_BASIC comment)
                               '^^xsd:string))
          (set gnt:symbol (field GeneRIF_BASIC symbol))
          (multiset dct:references
                    (map
                     (lambda (el)
                       (if (string-null? el)
                           ""
                           (ontology 'pubmed: el)))
                     (string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
                                   #\,)))
          (set gnt:hasVersion
               (format #f "~a" (field GeneRIF_BASIC VersionId)))
          (set dct:created
               (let ((createtime (field GeneRIF_BASIC createtime)))
                 (if (string? createtime)
                     ""
                     (annotate-field
                      (time-unix->string
                       createtime "~5")
                      '^^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 "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#>")
      ("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/>")
      ("ncbiTaxon:" "<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
     genewiki-symbols
     gn-genewiki-entries
     ncbi-genewiki-entries))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))