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#! /usr/bin/env guile
!#
(use-modules (rnrs programs)
(rnrs io ports)
(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-genofreeze
(tables (GenoFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
(left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
"WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
(schema-triples
(gn-term:datasetOfInbredSet rdfs:range gn:inbredSet)
(gn:genotypeDataset rdfs:subPropertyOf gn:dataset)
(gn-term:shortName rdfs:range rdfs:Literal))
(triples
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field GenoFreeze Name)
'pre "_" 'post)
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:genotypeDataset)
(set gn-term:name (field GenoFreeze Name))
(set gn-term:fullName (field GenoFreeze FullName))
(set gn-term:shortName (field GenoFreeze ShortName))
(set dct:created (annotate-field
(field GenoFreeze CreateTime)
'^^xsd:date))
(set gn-term:datasetOfInbredSet
(string->identifier "" (field InbredSet Name InbredSetName)))))
(define-dump dump-genotypes
(tables (Geno
(left-join GenoXRef "ON Geno.Id = GenoXRef.GenoId")
(left-join GenoFreeze "ON GenoFreeze.Id = GenoXRef.GenoFreezeId")
(left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")))
(schema-triples
(gn:genotype rdfs:range rdfs:Literal)
(gn-term:genotypeDataset rdfs:subPropertyOf gn:dataset))
(triples
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, ':')), Geno.Name)" abbrev))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:genotype)
(set gn-term:name (sanitize-rdf-string (field Geno Name)))
(set gn-term:markerName (sanitize-rdf-string (field Geno Marker_Name)))
(set gn-term:chr (field Geno Chr))
(set gn-term:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
(set gn-term:sequence (field Geno Sequence))
(set gn-term:source (field Geno Source))
(set gn-term:source2 (field Geno Source2))
(set gn-term:genotypeOfDataset
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(GenoFreeze.Name, '')" DatasetName))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
)
(set gn-term:chrNum
(annotate-field
(field ("IFNULL(Geno.chr_num, '')" chr_num))
'^^xsd:int))
(set gn:comments (field ("CAST(CONVERT(BINARY CONVERT(Geno.Comments USING latin1) USING utf8) AS VARCHAR(255))" Comments)))
(set gn-term:cM
(annotate-field
(field ("IFNULL(GenoXRef.cM, '')" Chr_mm8))
'^^xsd:int))))
(dump-with-documentation
(name "Genotype Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dct:" "<http://purl.org/dc/terms/>")
("gn:" "<http://genenetwork.org/id/>")
("gn-term:" "<http://genenetwork.org/term/>")
("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-genofreeze
dump-genotypes))
(outputs
'(#:documentation "./docs/dump-genotype.md"
#:rdf "./verified-data/dump-genotype.ttl")))
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