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#! /usr/bin/env guile
!#
(use-modules (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 publication
(tables (Publication))
(triples
(let ((pmid (field
("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
pmid)))
(publication-id (field Publication Id)))
(if (string-null? pmid)
(string->identifier "unpublished"
(number->string publication-id))
(ontology 'pubmed: pmid)))
(set rdf:type 'fabio:ResearchPaper)
(set fabio:hasPubMedId
(ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId))))
(set dct:title (delete-substrings (field Publication Title)
"Unknown"))
(set fabio:Journal (delete-substrings (field Publication Journal)
"Unknown"))
(set prism:volume (delete-substrings (field Publication Volume)
"Unknown"))
(set fabio:page (delete-substrings (field Publication Pages)
"Unknown"))
(set prism:publicationDate (annotate-field
(delete-substrings (field Publication Month)
"Unknown")
'^^xsd:gMonth))
(set fabio:hasPublicationYear
(annotate-field
(field
("IF(Publication.Year = 0, NULL, Publication.Year)" Year))
'^^xsd:gYear))
(multiset dct:creator
;; The authors field is a comma
;; separated list. Split it.
(map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,)))
(set dct:abstract
(sanitize-rdf-string
(field Publication Abstract)))))
(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 "Publications Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("gnt:" "<http://genenetwork.org/terms/>")
("fabio:" "<http://purl.org/spar/fabio/>")
("dct:" "<http://purl.org/dc/terms/>")
("prism:" "<http://prismstandard.org/namespaces/basic/2.0/>")
("gn:" "<http://genenetwork.org/id/>")
("gnc:" "<http://genenetwork.org/category/>")
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")))
(inputs
(list publication))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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