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#! /usr/bin/env guile
!#
(use-modules (rnrs programs)
(rnrs io ports)
(srfi srfi-1)
(srfi srfi-26)
(ice-9 getopt-long)
(ice-9 match)
(ice-9 regex)
(transform strings)
(transform sql)
(transform triples)
(transform special-forms))
(define-transformer gn:set->gn:dataset
(tables (Species
(inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
(inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id"))
"WHERE PublishFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, PublishFreeze.ShortName")
(triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
(multiset gnt:has_phenotype_data
(map (cut string->identifier "dataset" <> #:separator "_")
(string-split
(field ("GROUP_CONCAT(PublishFreeze.Name SEPARATOR ',')"
dataset_name))
#\,)))))
(define-transformer gn:dataset->gn:set
(tables (Datasets
(inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId")
(inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId")
(inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id"))
"WHERE PublishFreeze.public > 0 GROUP BY Datasets.DatasetId")
(triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")
(set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
(define-transformer gn:dataset->metadata
(tables (PublishXRef
(inner-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
(inner-join Species "ON InbredSet.SpeciesId = Species.Id")
(inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")
(inner-join Publication "ON Publication.Id = PublishXRef.PublicationId")
(inner-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))
"WHERE InbredSet.public > 0 GROUP BY Species.Name, PublishFreeze.Name")
(triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")
(set dct:created (annotate-field (field PublishFreeze CreateTime) '^^xsd:datetime))
(set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
(define-transformer gn:dataset->gn:trait
(tables (PublishXRef
(inner-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
(inner-join Species "ON InbredSet.SpeciesId = Species.Id")
(inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")
(inner-join Publication "ON Publication.Id = PublishXRef.PublicationId")
(inner-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))
"WHERE InbredSet.public > 0")
(triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")
(set gnt:has_phenotype_trait
(let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
(pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
(post-desc (blank-p (field Phenotype Post_publication_description)))
(pre-desc (blank-p (field Phenotype Post_publication_description))))
(string->identifier
"trait"
(format #f "~a_~a" (field PublishFreeze Name)
(or post-abbrev pre-abbrev post-desc pre-desc))
#:separator "_")))
(set dct:created (annotate-field (field PublishFreeze CreateTime) '^^xsd:datetime))
(set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
(let* ((option-spec
'((settings (single-char #\s) (value #t))
(output (single-char #\o) (value #t))
(documentation (single-char #\d) (value #t))))
(options (getopt-long (command-line) option-spec))
(settings (option-ref options 'settings #f))
(output (option-ref options 'output #f))
(documentation (option-ref options 'documentation #f))
(%connection-settings
(call-with-input-file settings
read)))
(with-documentation
(name "Phenotype Datasets")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dcat:" "<http://www.w3.org/ns/dcat#>")
("dct:" "<http://purl.org/dc/terms/>")
("gn:" "<http://rdf.genenetwork.org/v1/id/>")
("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
(list
gn:set->gn:dataset
gn:dataset->gn:set
gn:dataset->metadata
gn:dataset->gn:trait))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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