#! /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 probesetxref->metadata
  (tables (ProbeSetXRef
           (inner-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")
           (inner-join ProbeSet "ON ProbeSet.Id = ProbeSetXRef.ProbeSetId"))
          "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1")
  (triples (string->identifier
            "probeset_data"
            (uri-encode
             (format #f "~a_~a" (field ProbeSetFreeze Name ProbeSetFreezeName) (field ProbeSet Name ProbeSetName))) #:separator "_")
    (set rdf:type 'gnc:molecular_trait_metadata)
    (set dcat:distribution
         (string->symbol
          (sanitize-rdf-string
           (format #f "gnd:~a.json"
                   (field ("CONCAT(ProbeSetFreeze.Name, '_', ProbeSet.Name)"
                           PublishFreeze))))) )
    (set gnt:has_probeset (string->identifier "probeset" (field ProbeSet Name ProbeSetName)))
    (set dcat:isPartOf (string->identifier "dataset" (field ProbeSetFreeze Name ProbeSetFreezeName)
                                           #:separator "_"))
    (set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
                                  '^^xsd:double))
    (set gnt:SE (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se))
                                '^^xsd:double))
    (set gnt:locus (sanitize-rdf-string (field ProbeSetXRef Locus)))
    (set gnt:lod_score (annotate-field
                        (field ("IFNULL((ProbeSetXRef.LRS/4.604), '')" lrs))
                        '^^xsd:double))
    (set gnt:pvalue (annotate-field
                        (field ("IFNULL((ProbeSetXRef.pValue), '')" pValue))
                        '^^xsd:double))
    (set gnt:additive (annotate-field
                        (field ("IFNULL((ProbeSetXRef.additive), '')" additive))
                        '^^xsd:double))
    (set gnt:h2 (annotate-field
                 (field ("IFNULL((ProbeSetXRef.h2), '')" h2))
                 '^^xsd:double))))



(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 Experiments Metadata")
      (connection %connection-settings)
      (table-metadata? #f)
      (total-rows (assoc-ref
                   (sql-find db "SELECT count(*) AS count from ProbeSetXRef")
                   "count"))
      (rows-per-chunk 1000000)
      (prefixes
       '(("dcat:" "<http://www.w3.org/ns/dcat#>")
         ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
         ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
         ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
         ("gnd:" "<https://cd.genenetwork.org/api3/lmdb/v1/data/traits/>")
         ("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_>")
         ("dcat:" "<http://www.w3.org/ns/dcat#>")
         ("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 probesetxref->metadata))
      (outputs
       `(#:documentation ,documentation
         #:rdf ,output))))))