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(define-module (transform triples)
#:use-module (ice-9 regex)
#:use-module (ice-9 match)
#:use-module (transform strings)
#:export (ontology
string->identifier
prefix
triple
scm->triples
annotate-field
remap-species-identifiers
string->binomial-name))
(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 (annotate-field field schema)
(let ([schema (cond ((symbol? schema)
(symbol->string schema))
((string? schema) schema)
(else
(error "Use a string/symbol")))]
[string-field (if (number? field) (number->string field) field)])
(if (or (and (string? string-field) (string-null? string-field))
(eq? string-field #f))
""
(string->symbol
(format #f "~s~a" string-field schema)))))
(define* (string->identifier
prefix str
#:optional #:key
(ontology "gn:")
(separator "")
(proc string-capitalize-first))
"Convert STR to a turtle identifier after replacing illegal
characters with an underscore and prefixing with gn:PREFIX."
(if (or (and (string? str) (string-null? str))
(eq? str #f))
""
(string->symbol
(string-append ontology prefix separator
(string-delete
(lambda (c)
(eq? c #\)))
(string-map (lambda (c)
(case c
((#\/ #\< #\> #\+ #\( #\space #\@) #\-)
(else c)))
(proc
(string-trim-right
(regexp-substitute/global
#f "_"
str
'pre "-" 'post) #\.))))))))
(define* (prefix prefix iri #:optional (ttl? #t))
(format #t
(if ttl?
"@prefix ~a ~a .~%"
"PREFIX ~a ~a ~%")
prefix iri))
(define (ontology prefix value)
(if (and (string? value) (string-null? value))
""
(string->symbol
`,(format #f "~a~a" prefix value))))
(define (triple subject predicate object)
(unless (or (string? subject)
(symbol? subject))
(error "Triple subject not a string or symbol:"
(list subject predicate object)))
(unless (or (string? predicate)
(symbol? predicate))
(error "Triple predicate not a string or symbol:"
(list subject predicate object)))
(unless (or (string? object)
(symbol? object)
(number? object))
(error "Triple object not a string, symbol or number:"
(list subject predicate object)))
(let ([pattern (match object
((or (? symbol? object)
(? (lambda (el) (string-match "^\\( .* \\)$" el)) object)
(? (lambda (el) (string-match "^\\[ .* \\]$" el)) object))
"~a ~a ~a .~%")
(_ "~a ~a \"~a\" .~%"))])
(format #t pattern subject predicate
(if (symbol? object) (symbol->string object) object))))
(define* (scm->triples alist id
#:optional
(fn triple))
(for-each (match-lambda
((predicate . object)
(when (cond
((string? object)
(not (string-blank? object)))
(else object))
(fn id predicate object))))
alist))
(define (string->binomial-name name)
(let ((binomial?
(string-match
"\\\(.+\\)"
name)))
(string->identifier
""
(if binomial?
(regexp-substitute/global
#f "[^[:space:]A-Za-z0-9:]"
(match:substring binomial?)
'pre "" 'post)
name)
#:separator ""
#:proc string-capitalize-first)))
|
