#! /usr/bin/env guile
!#
(use-modules (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-publication
(tables (Publication))
(schema-triples
(gn-term:pubMedId rdfs:range rdfs:Literal)
(gn-term:title rdfs:range rdfs:Literal)
(gn-term:journal rdfs:range rdfs:Literal)
(gn-term:volume rdfs:range rdfs:Literal)
(gn-term:pages rdfs:range rdfs:Literal)
(gn-term:month rdfs:range rdfs:Literal)
(gn-term:year rdfs:range rdfs:Literal)
(gn-term:author rdfs:range rdfs:Literal)
(gn-term:abstract rdfs:range rdfs:Literal))
(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identifier "unpublished"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 'publication: pmid)))
(set rdf:type 'gn:publication)
(set gn-term:pubMedId
(ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId))))
(set gn-term:title (delete-substrings (field Publication Title)
"Unknown"))
(set gn-term:journal (delete-substrings (field Publication Journal)
"Unknown"))
(set gn-term:volume (delete-substrings (field Publication Volume)
"Unknown"))
(set gn-term:pages (delete-substrings (field Publication Pages)
"Unknown"))
(set gn-term:month (delete-substrings (field Publication Month)
"Unknown"))
(set gn-term:year (field Publication Year))
(multiset gn:author
;; The authors field is a comma
;; separated list. Split it.
(map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,)))
(set gn:abstract
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Publication.Abstract USING latin1) USING utf8) AS VARCHAR(100))" Abstract))))))
(dump-with-documentation
(name "Publications Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("gn-term:" "")
("gn:" "")
("publication:" "")
("pubmed:" "")
("rdfs:" "")
("rdf:" "")))
(inputs
(list dump-publication))
(outputs
'(#:documentation "./docs/dump-publication.md"
#:rdf "./verified-data/dump-publication.md")))