#! /usr/bin/env guile
!#

(use-modules (srfi srfi-1)
             (srfi srfi-26)
             (ice-9 match)
             (ice-9 regex)
             (transform strings)
             (transform sql)
             (transform triples)
             (transform special-forms))



(define %connection-settings
  (call-with-input-file (list-ref (command-line) 1)
    read))



(define-transformer probeset-data
  (tables (ProbeSetXRef
           (left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
           (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"))
          "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1")
  (schema-triples
   (gnc:probesetStatistics a skos:Concept)
   (gnc:probesetStatistics
    skos:description
    "This is a set of controlled terms that are used to describe a given probeset's statistics")
   (gnt:mean rdfs:domain gnc:probeset)
   (gnt:locus rdfs:domain gnc:probeset)
   (gnt:LRS rdfs:domain gnc:probeset)
   (gnt:stdErr rdfs:domain gnc:probeset)
   (gnt:stdErr rdfs:range xsd:double)
   (gnt:pValue rdfs:domain gnc:probeset)
   (gnt:pValue rdfs:range xsd:double)
   (gnt:h2 rdfs:domain gnc:probeset)
   (gnt:h2 rdfs:range xsd:double))
  (triples
      (string->identifier
       ""
       (regexp-substitute/global
        #f "[^A-Za-z0-9:]"
        (field
         ("CONCAT(ProbeSetFreeze.Name, '_', IF(NULLIF(TRIM(ProbeSet.Name), ProbeSet.Id) IS NULL, '', TRIM(ProbeSet.Name)))"
          probesetData))
        'pre "_" 'post)
       #:separator ""
       #:proc string-capitalize-first)
    (set rdf:type 'gnc:probesetStatistics)
    (set gnt:hasProbeSet (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 gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
                                  '^^xsd:double))
    (set gnt:locus (field ProbeSetXRef Locus))
    (set gnt:LRS (annotate-field
                  (field ("IFNULL(ProbeSetXRef.LRS, '')" lrs))
                  '^^xsd:double))
    (set gnt:additive
         (annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
                         '^^xsd:double))
    (set gnt:stdErr (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" stdErr))
                                    '^^xsd:double))
    (set gnt:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
                                    '^^xsd:double))
    (set gnt:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
                                '^^xsd:double))))



(with-documentation
 (name "Probeset Summary Statistics")
 (connection %connection-settings)
 (table-metadata? #f)
 (prefixes
  '(("gn:" "<http://genenetwork.org/id/>")
    ("gnc:" "<http://genenetwork.org/category/>")
    ("gnt:" "<http://genenetwork.org/id/>")
    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
    ("owl:" "<http://www.w3.org/2002/07/owl#>")
    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
 (inputs
  (list probeset-data))
 (outputs
  '(#:documentation "./docs/probeset-summary-stats.md"
    #:rdf "./verified-data/probeset-summary-stats.ttl")))