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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-directory
(list-ref (command-line) 2))
;; One email ID in the Investigators table has spaces in it. This
;; function fixes that.
(define (fix-email-id email)
(string-delete #\space email))
(define (investigator-attributes->id first-name last-name email)
;; There is just one record corresponding to "Evan Williams" which
;; does not have an email ID. To accommodate that record, we
;; construct the investigator ID from not just the email ID, but
;; also the first and the last names. It would be preferable to just
;; find Evan Williams' email ID and insert it into the database.
(string->identifier "investigator"
(string-join
;; Add special case for Yohan Bossé whose name
;; has unprintable characters.
;; TODO: Fix Yohan Bossé's name in the database.
(let ((last-name (if (string=? first-name "Yohan")
"Bosse"
last-name)))
(list first-name last-name (fix-email-id email)))
"_")))
(define-dump dump-investigators
;; There are a few duplicate entries. We group by email to
;; deduplicate.
(tables (Investigators)
"GROUP BY Email")
(schema-triples
;; TODO: Are ranges required for FOAF predicates? Can they not be
;; obtained from the FOAF spec?
(foaf:name rdfs:range rdfs:Literal)
(foaf:givenName rdfs:range rdfs:Literal)
(foaf:familyName rdfs:range rdfs:Literal)
(foaf:homepage rdfs:range rdfs:Literal)
(gn:address rdfs:range rdfs:Literal)
(gn:city rdfs:range rdfs:Literal)
(gn:state rdfs:range rdfs:Literal)
(gn:zipCode rdfs:range rdfs:Literal)
(gn:country rdfs:range rdfs:Literal))
(triples (investigator-attributes->id (field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email))
(set rdf:type 'foaf:Person)
(set foaf:name (string-append (field Investigators FirstName) " "
(if (string=? (field Investigators FirstName) "Yohan")
"Bossé"
(field Investigators LastName))))
(set foaf:givenName
(field ("CAST(CONVERT(BINARY CONVERT(FirstName USING latin1) USING utf8) AS VARCHAR(100))" FirstName)))
(set foaf:familyName
(field ("CAST(CONVERT(BINARY CONVERT(LastName USING latin1) USING utf8) AS VARCHAR(100))" LastName)))
(set foaf:homepage (field Investigators Url))
(set gn:address (field Investigators Address))
(set gn:city (field Investigators City))
(set gn:state (field Investigators State))
(set gn:zipCode (field Investigators ZipCode))
(set gn:country (field Investigators Country))))
(define-dump dump-info-files
(tables (InfoFiles
(left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
(left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name")
(left-join ProbeSetFreeze "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
(left-join InbredSet "ON InfoFiles.InbredSetId = InbredSet.InbredSetId")
(left-join Datasets "USING (DatasetId)")
(left-join DatasetStatus "USING (DatasetStatusId)")
(left-join Tissue "USING (TissueId)")
(left-join Investigators "USING (InvestigatorId)")
(left-join AvgMethod "USING (AvgMethodId)")
(left-join GeneChip "USING (GeneChipId)"))
"WHERE GN_AccesionId IS NOT NULL AND ((PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1) OR (GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1) OR (ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1))")
(schema-triples
(gn:datasetOfInvestigator rdfs:domain gn:dataset)
(gn:datasetOfInvestigator rdfs:range foaf:Person)
(gn:datasetOfInbredSet rdfs:domain gn:dataset)
(gn:datasetOfInbredSet rdfs:range gn:inbredSet)
(gn:datasetOfTissue rdfs:domain gn:dataset)
(gn:datasetOfTissue rdfs:range gn:tissue)
(gn:normalization rdfs:domain gn:dataset)
(gn:normalization rdfs:range gn:avgMethod)
(gn:datasetOfPlatform rdfs:domain gn:dataset)
(gn:datasetOfPlatform rdfs:range gn:geneChip)
(gn:accessionId rdfs:range rdfs:Literal)
(gn:datasetStatusName rdfs:range rdfs:Literal)
(gn:summary rdfs:range rdfs:Literal)
(gn:aboutTissue rdfs:range rdfs:Literal)
(gn:geoSeries rdfs:range rdfs:Literal)
(gn:name rdfs:range rdfs:Literal)
(gn:title rdfs:range rdfs:Literal)
(gn:specifics rdfs:range rdfs:Literal)
(gn:datasetGroup rdfs:range rdfs:Literal)
(gn:aboutCases rdfs:range rdfs:Literal)
(gn:aboutPlatform rdfs:range rdfs:Literal)
(gn:aboutDataProcessing rdfs:range rdfs:Literal)
(gn:notes rdfs:range rdfs:Literal)
(gn:experimentDesign rdfs:range rdfs:Literal)
(gn:contributors rdfs:range rdfs:Literal)
(gn:citation rdfs:range rdfs:Literal)
(gn:acknowledgment rdfs:range rdfs:Literal))
(triples (ontology 'dataset:
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field InfoFiles InfoPageName)
'pre "_" 'post))
;; Add GeneChipName and GeoPlatform:
;; GeneChip.GeneChipName AS gene_chip_name
;; GeneChip.GeoPlatform AS geo_platform
(set rdf:type (string->symbol
(field ("IF(GenoFreeze.Id IS NOT NULL, 'gn:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gn:phenotypeDataset', 'gn:dataset'))"
rdfType))))
(set gn:name (field InfoFiles InfoPageName))
(set dct:created
(field ("IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, '')))"
createTimeGenoFreeze)))
(set gn:datasetOfInvestigator
(investigator-attributes->id (field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email)))
(set gn:accessionId (string-append "GN" (number->string
(field InfoFiles GN_AccesionId))))
(set gn:datasetStatusName (string-downcase
(field DatasetStatus DatasetStatusName)))
(set gn:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))
(set gn:datasetOfTissue (string->identifier "tissue"
(field Tissue Short_Name)))
(set gn:normalization
(string->identifier "avgmethod"
;; If AvgMethodName is NULL, assume N/A.
(if (string-blank? (field AvgMethod Name AvgMethodName))
"N/A" (field AvgMethod Name AvgMethodName))))
(set gn:datasetOfPlatform
(string->identifier "platform"
(field GeneChip Name GeneChip)))
(set gn:summary
(sanitize-rdf-string (field Datasets Summary)))
(set gn:aboutTissue
(sanitize-rdf-string (field Datasets AboutTissue)))
(set gn:geoSeries
(and (not (string-prefix-ci? "no geo series"
(field Datasets GeoSeries)))
(field Datasets GeoSeries)))
(set gn:title (field InfoFiles Title))
(set gn:specifics (sanitize-rdf-string (field InfoFiles Specifics)))
(set gn:datasetGroup (field Datasets DatasetName DatasetGroup))
(set gn:aboutCases (sanitize-rdf-string (field Datasets AboutCases)))
(set gn:aboutPlatform (sanitize-rdf-string (field Datasets AboutPlatform)))
(set gn:aboutDataProcessing (sanitize-rdf-string
(field Datasets AboutDataProcessing)))
(set gn:notes (sanitize-rdf-string (field Datasets Notes)))
(set gn:experimentDesign (sanitize-rdf-string
(field Datasets ExperimentDesign)))
(set gn:contributors (sanitize-rdf-string (field Datasets Contributors)))
(set gn:citation (sanitize-rdf-string (field Datasets Citation)))
(set gn:acknowledgment (sanitize-rdf-string
(field Datasets Acknowledgment)))))
(call-with-target-database
%connection-settings
(lambda (db)
(with-output-to-file (string-append %dump-directory "dump-info-pages.ttl")
(lambda ()
(prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
(prefix "dct:" "<http://purl.org/dc/terms/>")
(prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
(prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
(prefix "gn:" "<http://genenetwork.org/>")
(prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
(prefix "homologene:" "<https://bio2rdf.org/homologene:>")
(prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
(prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
(prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
(prefix "omim:" "<https://www.omim.org/entry/>")
(prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
(prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
(prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
(prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
(prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
(prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
(prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
(prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
(prefix "up:" "<http://purl.uniprot.org/core/>")
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
(prefix "dataset:" "<http://genenetwork.org/dataset/>")
(newline)
(dump-info-files db)
(dump-investigators db))
#:encoding "utf8")))
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