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#! /usr/bin/env guile
!#
(use-modules (ice-9 getopt-long)
(transform triples)
(transform schema)
(transform special-forms)
(transform sql)
(transform table))
(define (call-with-genenetwork-database connection-settings proc)
(call-with-database "mysql" (string-join
(list (assq-ref connection-settings 'sql-username)
(assq-ref connection-settings 'sql-password)
(assq-ref connection-settings 'sql-database)
"tcp"
(assq-ref connection-settings 'sql-host)
(number->string
(assq-ref connection-settings 'sql-port)))
":")
proc))
(define (transform-table-schema connection-settings db)
(let ((tables (tables connection-settings db)))
(for-each (lambda (table)
(let ((table-id (string->identifier
"table"
;; We downcase table names in
;; identifiers. So, we distinguish
;; between the user and User tables.
(if (string=? (table-name table) "User")
"user2"
(table-name table)))))
(triple table-id 'rdf:type 'gn:sqlTable)
(triple table-id 'gn:name (table-name table))
(triple table-id 'gn:hasSize (string->symbol (format #f "~a" (table-size table))))
(for-each (lambda (column)
(let ((column-id (column-id (table-name table)
(column-name column))))
(triple column-id 'rdf:type 'gn:sqlTableField)
(triple column-id 'gn:name (column-name column))
(triple column-id 'gn:sqlFieldType (column-type column))
(triple table-id 'gn:hasField column-id)))
(table-columns table))))
tables)))
(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)))
(call-with-genenetwork-database
%connection-settings
(lambda (db)
(with-output-to-file output
(lambda ()
(prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
(prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
(prefix "gn:" "<http://genenetwork.org/id/>")
(prefix "gnc:" "<http://genenetwork.org/category/>")
(prefix "gnt:" "<http://genenetwork.org/term/>")
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
(prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
(newline)
(transform-table-schema %connection-settings db))))))
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