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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 (remap-species-identifiers str)
"This procedure remaps identifiers to standard binominal. Obviously this should
be sorted by correcting the database!"
(match str
["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
["Macaca mulatta" "Macaca nemestrina"]
["Bat (Glossophaga soricina)" "Glossophaga soricina"]
[str str]))
(define-transformer genotypes
(tables (Geno
(left-join Species "USING (SpeciesId)")))
(schema-triples
(gnc:genotype a skos:Concept)
(gnc:genotype
skos:description
"This is a set of controlled terms that are used to describe a given genotype")
(gnt:chr a owl:ObjectProperty)
(gnt:chr skos:description "This resource is located on a given chromosome")
(gnt:chr rdfs:domain gnc:genotype)
(gnt:mb a owl:ObjectProperty)
(gnt:mb skos:definition "The size of this resource in Mb")
(gnt:mb rdfs:domain gnc:genotype)
(gnt:mbMm8 a owl:ObjectProperty)
(gnt:mbMm8 skos:definition "TODO")
(gnt:mbMm8 rdfs:domain gnc:genotype)
(gnt:mb2016 a owl:ObjectProperty)
(gnt:mb2016 skos:definition "TODO")
(gnt:mb2016 rdfs:domain gnc:genotype)
(gnt:hasSequence a owl:ObjectProperty)
(gnt:hasSequence skos:definition "This resource has a given sequence")
(gnt:hasSequence rdfs:domain gnc:genotype)
(gnt:hasSource a owl:ObjectProperty)
(gnt:hasSource rdfs:domain gnc:genotype)
(gnt:hasSource skos:definition "This resource was obtained from this given source")
(gnt:hasAltSourceName a owl:ObjectProperty)
(gnt:hasAltSourceName rdfs:domain gnc:genotype)
(gnt:hasAltSourceName
skos:definition
"The alternative name this resource was obtained from")
(gnt:chrNum a owl:ObjectProperty)
(gnt:chrNum rdfs:domain gnc:genotype)
(gnt:chrNum skos:definition "The chromosome number for this resource")
(gnt:chrNum skos:definition "The chromosome number for this resource"))
(triples
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field Geno Name)
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:genotype)
(set skos:prefLabel (sanitize-rdf-string (field Geno Name)))
(set gnt:chr (field Geno Chr))
(set gnt:mb (annotate-field
(field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
(set gnt:mbMm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8))
'^^xsd:double))
(set gnt:mb2016
(annotate-field (field ("IFNULL(Geno.Mb_2016, '')" Mb_2016))
'^^xsd:double))
(set gnt:hasSequence (field Geno Sequence))
(set gnt:hasSource (field Geno Source))
;; Only transform Source2 if it differs from Source
(set gnt:hasAltSourceName
(field ("IF((Source2 = Source), NULL, Source2)"
Source2)))
(set gnt:belongsToSpecies
(string->identifier
"" (remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first))
(set gnt:chrNum
(annotate-field
(field Geno chr_num)
'^^xsd:int))
(set rdfs:comments (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 "Genotype Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dct:" "<http://purl.org/dc/terms/>")
("gn:" "<http://genenetwork.org/id/>")
("gnc:" "<http://genenetwork.org/category/>")
("gnt:" "<http://genenetwork.org/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#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
(list genotypes))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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