#! /usr/bin/env guile
!#

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



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



(define-dump dump-probeset-data
  (tables (ProbeSetXRef
           (left-join ProbeSet "ON ProbeSet.Id = ProbeSetXRef.ProbeSetId")
           (left-join ProbeSetFreeze "ON ProbeSet.ProbeSetFreezeId = ProbeSetFreeze.Id")))
  "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1"
  (schema-triples
   (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 (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))"
                             ProbeSetIdName)))
                 (probeset-id (field ProbeSet Id)))
             (if (string-null? id)
                 (string->identifier
                  "probeset"
                  (number->string
                   probeset-id))
                 (string->identifier
                  ""
                  (regexp-substitute/global
                   #f "[^A-Za-z0-9:]"
                   id
                   'pre "_" 'post)
                  #:separator ""
                  #:proc string-capitalize-first)))
    (set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
                                  '^^xsd:double))
    (set gnt:locus (field PublishXRef 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))
    (set gnt:belongsToDataset
         (string->identifier
          ""
          (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                    (field ProbeSetFreeze Name)
                                    'pre "_" 'post)
          #:separator ""
          #:proc string-capitalize-first))))



(dump-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/>")
    ("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 dump-probeset-metadata))
 (outputs
  '(#:documentation "./docs/dump-probeset-summary-stats.md"
    #:rdf "./verified-data/dump-probeset-summary-stats.ttl")))