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#! /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-probeset
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
(schema-triples
(gn-term:name rdfs:range rdfs:Literal)
(gn-term:probeset rdfs:range rdfs:Literal))
(triples (ontology
'probeset:
(string-trim-both
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(NULLIF(TRIM(ProbeSet.Name), ''), ProbeSet.Id)"
name))
'pre "_" 'post)))
(set rdf:type 'gn-id:probeset)
(set gn-term:chipOf (string->identifier "platform" (field GeneChip Name)))
(set gn-term:name (field ProbeSet Name))
(set gn-term:symbol (delete-substrings (field ProbeSet Symbol) "\""))
(set gn-term:description (sanitize-rdf-string
(field ProbeSet description)))
(set gn-term:chr (field ProbeSet Chr))
(set gn-term:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
(set gn-term:blatSeq (sanitize-rdf-string
(string-trim-both (field ProbeSet BlatSeq))))
(set gn-term:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
(set gn-term:uniProtReference (ontology 'uniprot:
(field ProbeSet UniProtID)))))
(dump-with-documentation
(name "ProbeSet Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("probeset:" "<http://genenetwork.org/probeset/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-r")
("uniprot:" "<http://purl.uniprot.org/uniprot/>")))
(inputs
(list dump-probeset))
(outputs
'(#:documentation "./docs/dump-probeset.md"
#:rdf "./verified-data/dump-probeset.ttl")))
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