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-rwxr-xr-xexamples/dump-dataset-metadata.scm50
1 files changed, 21 insertions, 29 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index 789e298..53c381c 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -16,9 +16,6 @@
(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
@@ -150,8 +147,7 @@
(field Investigators Email)))
(set gn:datasetOfOrganization
(field ("CAST(CONVERT(BINARY CONVERT(Organizations.OrganizationName USING latin1) USING utf8) AS VARCHAR(1500))" Organizations)))
- (set gn:accessionId (string-append "GN" (number->string
- (field InfoFiles GN_AccesionId))))
+ (set gn:accessionId (format #f "GN~a" (field InfoFiles GN_AccesionId)))
(set gn:datasetStatusName (string-downcase
(field DatasetStatus DatasetStatusName)))
(set gn:datasetOfInbredSet
@@ -234,27 +230,23 @@
-(call-with-target-database
- %connection-settings
- (lambda (db)
- (with-output-to-file (string-append %dump-directory "dump-info-pages.ttl")
- (lambda ()
- (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 "geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
- (prefix "gn:" "<http://genenetwork.org/>")
- (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
- (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
- (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 "uniprot:" "<http://purl.uniprot.org/uniprot/>")
- (prefix "up:" "<http://purl.uniprot.org/core/>")
- (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
- (prefix "probeset:" "<http://genenetwork.org/probeset/>")
- (prefix "dataset:" "<http://genenetwork.org/dataset/>")
- (newline)
- (dump-info-files db)
- (dump-investigators db))
- #:encoding "utf8")))
+(dump-with-documentation
+ (name "Info files / Investigators Metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+ (("dct:" "<http://purl.org/dc/terms/>")
+ ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
+ ("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/>")
+ ("foaf:" "<http://xmlns.com/foaf/0.1/>")
+ ("taxon:" "<http://purl.uniprot.org/taxonomy/>")
+ ("dataset:" "<http://genenetwork.org/dataset/>")))
+ (inputs
+ (dump-info-files
+ dump-investigators))
+ (outputs
+ (#:documentation "./docs/dump-info-pages.md"
+ #:rdf "./verified-data/dump-info-pages.ttl")))
+