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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:markers/snps->metadata
(tables (Geno
(inner-join Species "ON Geno.SpeciesId = Species.Id"))
"WHERE Species.Name != 'monkey'")
(triples (string->identifier "marker" (field Geno Name) #:separator "_")
(set gnt:has_species
(string->identifier "" (remap-species-identifiers (field Species Fullname))))
(set rdf:type 'gnc:dna_marker)
(set skos:prefLabel (field Geno Name))
(set skos:altLabel (field Geno Marker_Name))
(set gnt:chr (field Geno Chr))
(set gnt:mb (annotate-field (field Geno Mb) '^^xsd:doubleg))
(set gnt:sequence (field Geno Sequence))
(set gnt:source (field Geno Source))
(set rdfs:comment (field Geno Comments))))
(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 "Phenotypes Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dcat:" "<http://www.w3.org/ns/dcat#>")
("dct:" "<http://purl.org/dc/terms/>")
("gn:" "<http://rdf.genenetwork.org/v1/id/>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
("gnd:" "<https://cd.genenetwork.org/lmdb/v1/data/traits/>")
("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("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#>")
("qb:" "<http://purl.org/linked-data/cube#>")
("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
(inputs
(list gn:markers/snps->metadata))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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