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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-metadata
(tables (ProbeSetXRef
(left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
(left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"))
"WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1")
(schema-triples
(gn:probesetData rdfs:range gn:probeset)
(gn-term:hasProbeset rdfs:range rdfs:Literal))
(triples
(string->identifier
"probesetData"
(field ("CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id))"
ProbeSetName)))
(set rdf:type 'gn:probesetData)
(set gn-term:hasProbeset
(ontology
'probeset:
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
name))
'pre "_" 'post)))
(set gn-term:probesetOfDataset
(ontology
'probeset:
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field ProbeSetFreeze Name)
'pre "_" 'post)))
(set gn-term:mean
(annotate-field
(field ("IFNULL(ProbeSetXRef.mean, '')" mean))
'^^xsd:double))
(set gn-term:se
(annotate-field
(field ("IFNULL(ProbeSetXRef.se, '')" se))
'^^xsd:double))
(set gn-term:locus (field ProbeSetXRef Locus))
(set gn:LRS
(annotate-field
(field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
'^^xsd:double))
(set gn-term:pValue
(annotate-field
(field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
'^^xsd:double))
(set gn-term:additive
(annotate-field
(field ("IFNULL(ProbeSetXRef.additive, '')" additive))
'^^xsd:double))
(set gn-term:h2
(annotate-field
(field ("IFNULL(ProbeSetXRef.h2, '')" h2))
'^^xsd:float))))
(dump-with-documentation
(name "Probeset Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
("gn-term:" "<http://genenetwork.org/id/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
(list dump-probeset-metadata))
(outputs
'(#:documentation "./docs/dump-probeset-metadata.md"
#:rdf "./verified-data/dump-probeset-metadata.ttl")))
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