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#! /usr/bin/env guile
!#
(use-modules (rnrs programs)
(rnrs io ports)
(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))
(define-transformer gn:genotype->metadata
(tables (InbredSet
(inner-join GenoFreeze "ON GenoFreeze.InbredSetId = InbredSet.Id")
(inner-join InfoFiles "ON InfoFiles.InbredSetId = InbredSet.Id"))
"WHERE GenoFreeze.public > 0 GROUP BY GenoFreeze.Id")
(schema-triples
(gnc:genotype a owl:Class)
(gnc:genotype a skos:Concept)
(gnc:genotype rdfs:label "A genotype."))
(triples (string->identifier "genotype" (field GenoFreeze Name) #:separator "_")
(set rdf:type 'gnc:genotype)
(set skos:prefLabel (field GenoFreeze FullName))
(set skos:altLabel (field GenoFreeze ShortName))
(set dct:created (annotate-field (field GenoFreeze CreateTime) '^^xsd:datetime))))
(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 "Genotype Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dct:" "<http://purl.org/dc/terms/>")
("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#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
(list gn:genotype->metadata))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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