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#! /usr/bin/env guile
!#
(use-modules (srfi srfi-1)
(srfi srfi-26)
(ice-9 match)
(ice-9 regex)
(transform strings)
(transform sql)
(transform triples)
(transform special-forms))
(define %connection-settings
(call-with-input-file (list-ref (command-line) 1)
read))
(define-transformer probeset-data
(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
(gnc:probesetStatistics a skos:Concept)
(gnc:probesetStatistics
skos:description
"This is a set of controlled terms that are used to describe a given probeset's statistics")
(gnt:mean rdfs:domain gnc:probeset)
(gnt:locus rdfs:domain gnc:probeset)
(gnt:LRS rdfs:domain gnc:probeset)
(gnt:stdErr rdfs:domain gnc:probeset)
(gnt:stdErr rdfs:range xsd:double)
(gnt:pValue rdfs:domain gnc:probeset)
(gnt:pValue rdfs:range xsd:double)
(gnt:h2 rdfs:domain gnc:probeset)
(gnt:h2 rdfs:range xsd:double))
(triples
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field
("CONCAT(ProbeSetFreeze.Name, '_', IF(NULLIF(TRIM(ProbeSet.Name), ProbeSet.Id) IS NULL, '', TRIM(ProbeSet.Name)))"
probesetData))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:probesetStatistics)
(set gnt:hasProbeSet (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))"
ProbeSetIdName)))
(probeset-id (field ProbeSet Id)))
(string->identifier
"probeset"
(if (string-null? id)
(number->string probeset-id)
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
id
'pre "_" 'post)))))
(set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
'^^xsd:double))
(set gnt:locus (field ProbeSetXRef Locus))
(set gnt:LRS (annotate-field
(field ("IFNULL(ProbeSetXRef.LRS, '')" lrs))
'^^xsd:double))
(set gnt:additive
(annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
'^^xsd:double))
(set gnt:stdErr (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" stdErr))
'^^xsd:double))
(set gnt:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
'^^xsd:double))
(set gnt:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
'^^xsd:double))))
(with-documentation
(name "Probeset Summary Statistics")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
("gnc:" "<http://genenetwork.org/category/>")
("gnt:" "<http://genenetwork.org/id/>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("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 probeset-data))
(outputs
'(#:documentation "./docs/probeset-summary-stats.md"
#:rdf "./verified-data/probeset-summary-stats.ttl")))
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