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#! /usr/bin/env guile
!#
(use-modules (rnrs programs)
(rnrs io ports)
(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))
;; Only dump publish freeze entries that were not dumped from the InfoFiles page
(define-dump dump-publishfreeze
(tables (PublishFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
(left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
"WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
(schema-triples
(gn-term:datasetOfInbredSet rdfs:range gn:inbredSet)
(gn-term:name rdfs:range rdfs:Literal)
(gn-term:fullName rdfs:range rdfs:Literal)
(gn-term:shortName rdfs:range rdfs:Literal)
(gn:phenotypeDataset rdf:subClassOf gn:dataset))
(triples
(string->identifier
""
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field PublishFreeze Name)
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:phenotypeDataset)
(set gn-term:name (field PublishFreeze Name))
(set gn-term:fullName (field PublishFreeze FullName))
(set gn-term:shortName (field PublishFreeze ShortName))
(set dct:created (annotate-field
(field PublishFreeze CreateTime)
'^^xsd:date))
(set gn-term:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
(define-dump dump-phenotypes
(tables (Phenotype
(left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId")
(left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
(left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
(left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
(schema-triples
(gn:phenotypeDataset rdfs:subPropertyOf gn:dataset)
(gn-term:publicationDescription rdfs:range rdfs:Literal)
(gn-term:originalDescription rdfs:range rdfs:Literal)
(gn-term:prePublicationDescription rdfs:range rdfs:Literal)
(gn-term:postPublicationAbbreviation rdfs:range rdfs:Literal)
(gn-term:labCode rdfs:range rdfs:Literal)
(gn-term:submitter rdfs:range rdfs:Literal)
(gn-term:owner rdfs:range rdfs:Literal)
(gn-term:mean rdfs:range xsd:double)
(gn-term:LRS rdfs:range xsd:float)
(gn-term:locus rdfs:range rdfs:Literal)
(gn-term:additive rdfs:range xsd:decimal)
(gn-term:sequence rdfs:range rdfs:Literal)
(gn-term:phenotypeOfPublication rdfs:range gn-term:pubMedId))
(triples (string->identifier
""
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:phenotype)
(set gn-term:name (sanitize-rdf-string
(field
("CAST(CONVERT(BINARY CONVERT(IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) USING latin1) USING utf8) AS VARCHAR(100))"
PhenotypeName))))
;; There is no row with an empty post-publication description so
;; use this field as the main publication description
(set gn-term:publicationDescription
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
postPubDescr))))
(set gn-term:originalDescription (sanitize-rdf-string
(delete-substrings
(field Phenotype Original_description)
"Original post publication description: ")))
(set gn-term:prePublicationDescription
(sanitize-rdf-string
(field
("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
prePubDesc))))
(set gn-term:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
(set gn-term:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
(set gn-term:labCode (field Phenotype Lab_code))
(set gn-term:submitter (sanitize-rdf-string (field Phenotype Submitter)))
(set gn-term:owner (sanitize-rdf-string (field Phenotype Owner)))
(set gn-term:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
'^^xsd:double))
(set gn-term:locus (field PublishXRef Locus))
(set gn-term:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
(set gn-term:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
(set gn-term:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
(set gn-term:phenotypeOfDataset
(string->identifier
""
(field
("IFNULL(InfoFiles.InfoPageName, IFNULL(PublishFreeze.Name, ''))" DatasetName))
#:separator ""
#:proc string-capitalize-first))
(set gn-term:phenotypeOfPublication
(let ((pmid (field
("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
pmid)))
(publication-id (field Publication Id)))
(if (string-null? pmid)
(string->identifier "unpublished"
(number->string publication-id))
(ontology 'pubmed: pmid))))))
(dump-with-documentation
(name "Phenotypes Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dct:" "<http://purl.org/dc/terms/>")
("gn:" "<http://genenetwork.org/id/>")
("gn-term:" "<http://genenetwork.org/terms/>")
("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#>")
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
(inputs
(list dump-publishfreeze
dump-phenotypes))
(outputs
'(#:documentation "./docs/dump-phenotype.md"
#:rdf "./verified-data/dump-phenotype.ttl")))
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