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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-species
(tables (Species))
(schema-triples
(gn:name rdfs:range rdfs:Literal)
(gn:displayName rdfs:range rdfs:Literal)
(gn:binomialName rdfs:range rdfs:Literal)
(gn:family rdfs:range rdfs:Literal))
(triples (string->identifier "species" (field Species FullName))
(set rdf:type 'gn:species)
(set gn:name (field Species SpeciesName))
(set gn:displayName (field Species MenuName))
(set gn:binomialName (field Species FullName))
(set gn:family (field Species Family))
(set gn:organism (ontology 'taxon: (field Species TaxonomyId)))))
(define-dump dump-strain
(tables (Strain
(left-join Species "ON Strain.SpeciesId = Species.SpeciesId")))
(schema-triples
(gn:strainOfSpecies rdfs:domain gn:strain)
(gn:strainOfSpecies rdfs:range gn:species)
(gn:name rdfs:range rdfs:Literal)
(gn:alias rdfs:range rdfs:Literal)
(gn:symbol rdfs:range rdfs:Literal))
(triples (string->identifier
"strain"
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000))" StrainName))
'pre "_" 'post))
(set rdf:type 'gn:strain)
(set gn:strainOfSpecies
(string->identifier "species" (field Species FullName)))
;; Name, and maybe a second name
(set gn:name (sanitize-rdf-string (field Strain Name)))
(set gn:name (sanitize-rdf-string (field Strain Name2)))
(set gn:alias (sanitize-rdf-string (field Strain Alias)))
(set gn:symbol (field Strain Symbol))))
(define-dump dump-mapping-method
(tables (MappingMethod))
(triples (string->identifier "mappingMethod" (field MappingMethod Name))
(set rdf:type 'gn:mappingMethod)))
(define-dump dump-inbred-set
(tables (InbredSet
(left-join Species "ON InbredSet.SpeciesId=Species.Id")
(left-join MappingMethod
"ON InbredSet.MappingMethodId=MappingMethod.Id")))
(schema-triples
(gn:fullName rdfs:range rdfs:Literal)
(gn:geneticType rdfs:range rdfs:Literal)
(gn:inbredSetCode rdfs:range rdfs:Literal)
(gn:inbredFamily rdfs:range rdfs:Literal)
(gn:inbredSetOfSpecies rdfs:range gn:species)
(gn:inbredSetType rdfs:range rdfs:Literal)
(gn:phenotype rdfs:range gn:inbredSetType)
(gn:genotype rdfs:range gn:inbredSetType)
(gn:inbredSetOfMappingMethod rdfs:range gn:mappingMethod))
(triples (string->identifier "inbredSet" (field InbredSet Name))
(set rdf:type 'gn:inbredSet)
(set gn:binomialName (field InbredSet FullName))
(set gn:geneticType (field InbredSet GeneticType))
(set gn:inbredFamily (field InbredSet Family))
(set gn:inbredSetOfMappingMethod (field MappingMethod Name))
(set gn:inbredSetCode (field InbredSet InbredSetCode))
(set gn:inbredSetOfSpecies
(string->identifier "species" (field Species FullName BinomialName)))
(set gn:genotype
(field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
(set gn:phenotype
(field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))))
(define-dump dump-avg-method
;; The Name and Normalization fields seem to be the same. Dump only
;; the Name field.
(tables (AvgMethod))
(schema-triples
(gn:name rdfs:range rdfs:Literal))
(triples (string->identifier "avgmethod" (field AvgMethod Name))
(set rdf:type 'gn:avgMethod)
(set gn:name (field AvgMethod Name))))
(dump-with-documentation
(name "Species Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
(("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("gn:" "<http://genenetwork.org/terms/>")
("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
(inputs
(dump-species
dump-strain
dump-mapping-method
dump-avg-method))
(outputs
(#:documentation "docs/dump-species-metadata.md"
#:rdf "./verified-data/dump-species-metadata.ttl")))
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