Re-introduce unique identifiers for RIF metadata.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 48 insertions, 71 deletions

diff --git a/examples/generif.scm b/examples/generif.scm
index 27fa388..1dfd224 100755
--- a/examples/generif.scm
+++ b/examples/generif.scm
@@ -34,78 +34,55 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol")
    (gnt:reason skos:definition "The reason why this resource was modified")
    (gnc:GNWikiEntry rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork")
    (gnt:geneSymbol rdfs:domain gnc:GNWikiEntry))
-  ;; We want to avoid manually generating a unique identifier for each
-  ;; comment.  As such we use a blank node (that has the comment) as
-  ;; the subject of the triples produced by matching the
-  ;; predicateObjectList production:
-  ;; <https://www.w3.org/TR/turtle/#grammar-production-predicateObjectList>
   (triples
-      (format #f "[ rdfs:label '''~a'''@en] "
-              (field GeneRIF comment))
-    (set rdf:type
-         (let* ((create-time (field
-                              ("CAST(createtime AS CHAR)" EntryCreateTime)))
-                (pmid (field GeneRIF PubMed_ID PMID))
-                (web-url (field GeneRIF weburl))
-                (species (string->identifier
-                          ""
-                          (remap-species-identifiers (field Species Fullname))
-                          #:separator ""
-                          #:proc string-capitalize-first))
-                (version-id (field GeneRIF versionId))
-                (identifier (field GeneRIF Id))
-                (initial (sanitize-rdf-string (field GeneRIF initial)))
-                (reason (field GeneRIF reason))
-                (email (sanitize-rdf-string (field GeneRIF email)))
-                (category
-                 (field ("GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR ';')"
-                         GeneCategory))))
-           (string->symbol
-            (string-append
-             (format #f "gnc:GNWikiEntry ;\n")
-             (if (string? species)
-                 ""
-                 (format #f "\tgnt:belongsToSpecies ~a ;\n"
-                         species))
-             (format #f "\tdct:created ~s^^xsd:datetime ;\n"
-                     create-time)
-             (if (and (string? pmid) (not (string-null? pmid)))
-                 (format #f
-                         "\tdct:references ( ~{pubmed:~a ~}) ;\n"
-                         (string-split pmid #\space))
-                 "\tdct:references rdf:nil ;\n")
-             (if (string-blank? email)
-                 ""
-                 (format #f "\tfoaf:mbox <~a> ;\n" email))
-             (format #f "\tdct:identifier \"~s\"^^xsd:integer ;\n" identifier)
-             (if (and (string? web-url) (not (string-null? web-url)))
-                 (format #f "\tfoaf:homepage <~a> ;\n"
-                         web-url)
-                 "")
-             (format #f "\tdct:hasVersion \"~s\"^^xsd:integer ;\n" version-id)
-             (if (or (null? initial)
-                     (string-blank? initial))
-                 "" (format #f "\tgnt:initial ~s ;\n" initial))
-             (if (string-blank? reason)
-                 ""
-                 (format #f "\tgnt:reason ~s ;\n" reason))
-             (if (string-blank? category)
-                 "\tgnt:belongsToCategory rdf:nil ;\n"
-                 (format #f
-                         "\tgnt:belongsToCategory ( ~{~s ~}) ;\n"
-                         (string-split category #\;)))
-             ;; We have this symbol at the very end of this transform
-             ;; because we have a strong guarantee that it will be a
-             ;; non-null value hence always terminating this triple
-             ;; properly with a "."
-             (format
-              #f "\tgnt:symbol ~a"
-              (string->identifier
-               "symbol"
-               (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                         (field GeneRIF symbol)
-                                         'pre "_" 'post)
-               #:proc (lambda (x) x)))))))))
+      (format
+       #f "gn:wiki-~a-~a"
+       (field GeneRIF Id)
+       (field GeneRIF versionId))
+    (set rdfs:label (string->symbol (format #f "'''~a'''@en" (field GeneRIF comment))))
+    (set rdf:type 'gnc:GNWikiEntry)
+    (set gnt:symbol (field GeneRIF symbol))
+    (set gnt:belongsToSpecies (string->identifier
+                               ""
+                               (remap-species-identifiers (field Species Fullname))
+                               #:separator ""
+                               #:proc string-capitalize-first))
+    (set dct:created
+         (string->symbol
+          (format #f "~s^^xsd:datetime "
+                  (field
+                   ("CAST(createtime AS CHAR)" EntryCreateTime)))))
+    (multiset dct:references
+              (map (lambda (pmid)
+                     (if (string-blank? pmid)
+                         ""
+                         (string->symbol
+                          (format #f "pubmed:~a" (string-trim-both pmid)))))
+                   (string-split (field GeneRIF PubMed_ID PMID)
+                                 #\space)))
+    (set foaf:mbox
+         (let ((mbox (sanitize-rdf-string (field GeneRIF email))))
+           (if (string-blank? mbox)
+               ""
+               (string->symbol
+                (format #f "<~a>" mbox)))))
+    (set dct:identifier (annotate-field (format #f "~s" (field GeneRIF Id))
+                                        '^^xsd:integer))
+    (set foaf:homepage
+         (let ((homepage (sanitize-rdf-string (field GeneRIF weburl))))
+            (if (string-blank? homepage)
+                ""
+                (string->symbol
+                 (format #f "<~a>" homepage)))))
+    (set dct:hasVersion (annotate-field (format #f "~s" (field GeneRIF versionId))
+                                        '^^xsd:integer))
+    (set gnt:initial (sanitize-rdf-string (field GeneRIF initial)))
+    (set gnt:reason (field GeneRIF reason))
+    (multiset gnt:belongsToCategory
+              (string-split
+               (field ("GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR ';')"
+                       GeneCategory))
+               #\;))))
 
 (define-transformer ncbi-genewiki-entries
   (tables (GeneRIF_BASIC