#! /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)
             (web uri))

(define-transformer probeset->metadata
  (tables (ProbeSet
           (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))
          "WHERE ProbeSet.Name IS NOT NULL AND TRIM(ProbeSet.Name) != ''")
  (triples
      (string->identifier "probeset" (field ProbeSet Name))
    (set rdf:type 'gnc:probeset)
    (set skos:prefLabel (field ProbeSet Name))
    (multiset skos:altLabel
              (map string-trim-both
                   (string-split (sanitize-rdf-string (field ProbeSet alias)) #\;)))
    (set gnt:uses_genechip (string->identifier "platform" (field GeneChip Name) #:separator "_"))
    (set gnt:has_target_id (string-trim-both (sanitize-rdf-string (field ProbeSet TargetId))))
    (set gnt:symbol (string-trim-both (field ProbeSet Symbol)))
    (set dct:description (sanitize-rdf-string (field ProbeSet description)))
    (set gnt:targets_region (string-trim-both (sanitize-rdf-string (field ProbeSet Probe_set_target_region))))
    (set gnt:chr (field ProbeSet Chr))
    (set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
    (set gnt:mb_mm8 (annotate-field (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))
                                    '^^xsd:double))
    (set gnt:has_specificity
         (field ("IFNULL(ProbeSet.Probe_set_specificity, '')"
                 Probe_set_specificity)))
    (set gnt:has_blat_score
         (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')"
                 Probe_set_BLAT_score)))
    (set gnt:has_blat_mb_start
         (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')"
                                 Probe_set_Blat_Mb_start))
                         '^^xsd:double))
    (set gnt:has_blat_mb_end
         (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')"
                                 Probe_set_Blat_Mb_end))
                         '^^xsd:double))
    (set gnt:has_blat_seq (sanitize-rdf-string (field ProbeSet BlatSeq)))
    (set gnt:has_target_seq (sanitize-rdf-string (field ProbeSet TargetSeq)))
    (set gnt:has_homologene_id (ontology 'homologene:
                                         (uri-encode
                                          (field ("IFNULL(ProbeSet.HomoloGeneID, '')"
                                                  HomoloGeneID)))))
    (set gnt:has_uniprot_id (ontology 'uniprot:
                                      (uri-encode
                                       (field ("IFNULL(ProbeSet.UniProtID, '')"
                                               UniProtID)))))
    (set gnt:has_pub_chem_id (ontology
                              'pubchem:
                              (uri-encode
                               (field ("IFNULL(ProbeSet.PubChem_ID, '')"
                                       PubChem_ID)))))
    (set gnt:has_kegg_id (ontology
                          'kegg:
                          (uri-encode
                           (field ("IFNULL(ProbeSet.KEGG_ID, '')"
                                   KEGG_ID)))))
    (set gnt:has_omim_id (ontology
                          'omim:
                          (uri-encode
                           (let ((omim (field ("IFNULL(ProbeSet.OMIM, '')"
                                               OMIM))))
                             (if (number? omim)
                                 omim
                                 (regexp-substitute/global
                                  #f "[^0-9]"
                                  omim
                                  'pre "" 'post))))))
    (set gnt:has_chebi_id (ontology
                           'chebi:
                           (uri-encode
                            (field ("IFNULL(ProbeSet.ChEBI_ID, '')"
                                    ChEBI_ID)))))))




(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)))
  (call-with-target-database
   %connection-settings
   (lambda (db)
     (with-documentation
      (name "ProbeSet Metadata")
      (connection %connection-settings)
      (table-metadata? #f)
      (total-rows (assoc-ref
                   (sql-find db "SELECT count(*) AS count from ProbeSet")
                   "count"))
      (rows-per-chunk 1000000)
      (prefixes
       '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
         ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
         ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
         ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
         ("kegg:" "<http://bio2rdf.org/ns/kegg#>")
         ("pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
         ("omim:" "<https://www.omim.org/entry/>")
         ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
         ("uniprot:" "<http://purl.uniprot.org/uniprot/>")
         ("chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
         ("dct:" "<http://purl.org/dc/terms/>")
         ("owl:" "<http://www.w3.org/2002/07/owl#>")
         ("homologene:" "<https://bio2rdf.org/homologene:>")
         ("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->metadata))
      (outputs
       `(#:documentation ,documentation
         #:rdf ,output))))))