#! /usr/bin/env guile
!#

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


(define-transformer probeset
  (tables (ProbeSet
           (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")
           (left-join Species "ON GeneChip.SpeciesId = Species.Id"))
          "WHERE ProbeSet.Name IS NOT NULL")
  (schema-triples
   (gnc:omimLink rdfs:Class gnc:ResourceLink)
   (gnc:omimLink rdfs:label "OMIM")
   (gnc:omimLink rdfs:comments "Summary from On Mendelion Inheritance in Man")
   (gnc:homologeneLink rdfs:Class gnc:ResourceLink)
   (gnc:homologeneLink rdfs:label "HomoloGene")
   (gnc:homologeneLink rdfs:comments "Find similar genes in other species")
   (gnc:uniprot a owl:ObjectProperty)
   (gnc:uniprot rdfs:label "UniProt")
   (gnc:uniprot rdfs:comments "UniProt resource")
   (gnt:hasChip a owl:ObjectProperty)
   (gnt:hasChip rdfs:domain gnc:Probeset)
   (gnt:hasTargetId a owl:ObjectProperty)
   (gnt:hasTargetId rdfs:domain gnc:Probeset)
   (gnt:geneSymbol rdfs:domain gnc:Probeset)
   (gnt:location rdfs:domain gnc:ProbeSet)
   (gnt:location a owl:ObjectProperty)
   (gnt:strandPosition rdfs:domain gnc:ProbeSet)
   (gnt:strandPosition a owl:ObjectProperty)
   (gnt:targetsRegion a owl:ObjectProperty)
   (gnt:targetsRegion rdfs:domain gnc:Probeset)
   (gnt:chr rdfs:domain gnc:Probeset)
   (gnt:mb rdfs:domain gnc:Probeset)
   (gnt:hasSpecificity a owl:ObjectProperty)
   (gnt:hasSpecificity rdfs:domain gnc:Probeset)
   (gnt:hasBlatScore a owl:ObjectProperty)
   (gnt:hasBlatScore rdfs:domain gnc:Probeset)
   (gnt:hasBlatMbStart a owl:ObjectProperty)
   (gnt:hasBlatMbStart rdfs:domain gnc:Probeset)
   (gnt:hasBlatMbEnd a owl:ObjectProperty)
   (gnt:hasBlatMbEnd rdfs:domain gnc:Probeset)
   (gnt:hasBlatSeq a owl:ObjectProperty)
   (gnt:hasBlatSeq rdfs:domain gnc:Probeset)
   (gnt:hasTargetSeq a owl:ObjectProperty)
   (gnt:hasTargetSeq rdfs:domain gnc:Probeset))
  (triples
      (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))"
                        ProbeSetIdName)))
            (probeset-id (field ProbeSet Id)))
        (string->identifier
         "probeset"
         (if (string-null? id)
             (number->string probeset-id)
             (regexp-substitute/global
              #f "[^A-Za-z0-9:]"
              id
              'pre "_" 'post))))
    (set rdf:type 'gnc:Probeset)
    (set rdfs:label (field ProbeSet Name))
    (set skos:altLabel
         (replace-substrings
          (field ProbeSet alias)
          '(("\r\n" . "; "))))
    (set gnt:hasChip
         (string->identifier
          "platform"
          (field ("IFNULL(GeneChip.Name, '')" GeneChipName))))
    (set gnt:hasTargetId
         (field ("NULLIF(TRIM(ProbeSet.TargetId), '')"
                 TargetId)))
    (set gnt:geneSymbol
         (field ProbeSet Symbol))
    (set dct:description (sanitize-rdf-string (field ProbeSet description)))
    (set gnt:targetsRegion
         (sanitize-rdf-string
          (field ("NULLIF(TRIM(ProbeSet.Probe_set_target_region), '')"
                  Probe_set_target_region))))
    (set gnt:chr (field ProbeSet Chr))
    (set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
    (set gnt:location
         (let* ((mb (field ProbeSet Mb))
                (chr (field ProbeSet Chr))
                (strand-probe (field ProbeSet Strand_Probe))
                (location (list chr mb)))
           (match location
             (("Un" mb)
              (format #f "Not available"))
             ((chr "")
              (if (string-blank? chr)
                  (format #f "Not available")
                  (format #f "Chr ~a @ Unknown position ~a~:[~;~a~]"
                          chr mb
                          (and (string? strand-probe) (or (string=? "+" strand-probe)
                                                          (string=? "-" strand-probe)))
                          (cond ((string=? "+" strand-probe)
                                 "on the plus strand")
                                ((string=? "-" strand-probe)
                                 "on the minus strand")
                                (else "")))))
             (_
              (format #f "Chr ~a @ ~a Mb ~:[~;~a~]"
                      chr mb
                      (and (string? strand-probe) (or (string=? "+" strand-probe)
                                                      (string=? "-" strand-probe)))
                      (cond ((string=? "+" strand-probe)
                             "on the plus strand")
                            ((string=? "-" strand-probe)
                             "on the minus strand")
                            (else "")))))))
    (set gnt:hasGeneId
         (ontology 'gene:
                   (string-trim-both (field ProbeSet GeneId))))
    ;; OMIM Link
    (set dct:references
         (let ((omim (field ProbeSet OMIM)))
           (if (not (string-blank? omim))
               (string->symbol
                (format #f
                        "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a"
                        "http://www.ncbi.nlm.nih.gov/omim/"
                        (uri-encode omim)
                        "a gnc:omimLink"))
               "")))
    ;; Homologene Link
    (set dct:references
         (let ((homologene (field ProbeSet HomoloGeneID)))
           (if (not (string-blank? homologene))
               (string->symbol
                (format #f
                        "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a"
                        "http://www.ncbi.nlm.nih.gov/homologene/?term="
                        (uri-encode homologene)
                        "a gnc:homologeneLink"))
               "")))
    (set gnt:uniprot
         (ontology 'uniprot: (field ProbeSet UniProtID)))
    (set gnt:strandProbe
         (field ProbeSet Strand_Probe))
    (set gnt:hasSpecificity
         (field ("IFNULL(ProbeSet.Probe_set_specificity, '')"
                 Probe_set_specificity)))
    (set gnt:hasBlatScore
         (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')"
                 Probe_set_BLAT_score)))
    (set gnt:hasBlatMbStart
         (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')"
                                 Probe_set_Blat_Mb_start))
                         '^^xsd:double))
    (set gnt:hasBlatMbEnd
         (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')"
                                 Probe_set_Blat_Mb_end))
                         '^^xsd:double))
    (set gnt:hasBlatSeq (sanitize-rdf-string (field ProbeSet BlatSeq)))
    (set gnt:hasTargetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))))




(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 "ProbeSet Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("gn:" "<http://genenetwork.org/id/>")
      ("probeset:" "<http://genenetwork.org/probeset/>")
      ("gnc:" "<http://genenetwork.org/category/>")
      ("gene:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
      ("gnt:" "<http://genenetwork.org/term/>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
      ("dct:" "<http://purl.org/dc/terms/>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
      ("qb:" "<http://purl.org/linked-data/cube#>")
      ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
   (inputs
    (list probeset))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))