Set string->identifier to defaut to "" sep and string-capitalize

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

4 files changed, 22 insertions, 51 deletions

diff --git a/examples/classification.scm b/examples/classification.scm
index 5d6840b..3843c49 100755
--- a/examples/classification.scm
+++ b/examples/classification.scm
@@ -47,9 +47,7 @@
    (gnc:Species xkos:depth "3")
    (gnc:Species xkos:specializes gnc:Set))
   (triples "gnc:Species"
-    (set skos:member (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                          #:separator ""
-                          #:proc string-capitalize-first))))
+    (set skos:member (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
 
 (define-transformer classification-scheme-set
   (tables (InbredSet))
@@ -61,9 +59,7 @@
   (triples "gnc:Set"
     (set skos:member
          (string->identifier
-          "set" (field InbredSet Name)
-          #:separator ""
-          #:proc string-capitalize-first))))
+          "set" (field InbredSet Name)))))
 
 (define-transformer species
   (tables (Species))
@@ -75,9 +71,7 @@
    (gnt:shortName rdfs:domain gnc:Species)
    (gnt:shortName skos:definition "The short name of a given resource"))
   (triples
-      (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                          #:separator ""
-                          #:proc string-capitalize-first)
+      (string->identifier "" (remap-species-identifiers (field Species Fullname)))
     (set skos:inScheme 'gnc:ResourceClassificationScheme)
     (set rdfs:label (remap-species-identifiers (field Species Fullname)))
     (set skos:prefLabel (field Species MenuName))
@@ -103,9 +97,7 @@
    (gnt:mappingMethod a owl:ObjectProperty)
    (gnt:mappingMethod rdfs:domain gnc:set))
   (triples (string->identifier
-            "set" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first)
+            "set" (field InbredSet Name))
     (set skos:inScheme 'gnc:ResourceClassificationScheme)
     (set rdfs:label (field InbredSet FullName))
     (set skos:prefLabel (field InbredSet Name))
diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
index 56280a7..e6ef350 100755
--- a/examples/dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -81,9 +81,7 @@
                                Title)))
     (set gnt:hasGOTreeValue (field GeneChip Go_tree_value))
     (set xkos:classifiedUnder
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                             #:separator ""
-                             #:proc string-capitalize-first))
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
     (set gnt:hasGeoSeriesId
          (ontology 'geoSeries:
                    (string-trim-both (field GeneChip GeoPlatform))))))
@@ -146,9 +144,7 @@
   (triples (string->identifier
             "" (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                          (field InfoFiles InfoPageName)
-                                         'pre "_" 'post)
-            #:separator ""
-            #:proc string-capitalize-first)
+                                         'pre "_" 'post))
     (set rdf:type 'dcat:Dataset)
     (set xkos:classifiedUnder
          (let ([dataset-type
@@ -190,9 +186,7 @@
                            (field DatasetStatus DatasetStatusName)))
     (set xkos:classifiedUnder
          (string->identifier
-          "set" (field InbredSet Name)
-          #:separator ""
-          #:proc string-capitalize-first))
+          "set" (field InbredSet Name)))
     (set gnt:hasTissue (string->identifier "tissue"
                                            (field Tissue Short_Name)))
     (set gnt:usesNormalization
@@ -253,9 +247,7 @@
        ""
        (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                  (field PublishFreeze Name)
-                                 'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
+                                 'pre "_" 'post))
     (set xkos:classifiedUnder 'gnc:Phenotype)
     (set dct:title  (field PublishFreeze FullName))
     (set rdfs:label (field PublishFreeze Name))
@@ -265,9 +257,7 @@
                       '^^xsd:date))
     (set xkos:classifiedUnder
          (string->identifier
-          "set" (field InbredSet Name)
-          #:separator ""
-          #:proc string-capitalize-first))))
+          "set" (field InbredSet Name)))))
 
 (define-transformer genofreeze
   (tables (GenoFreeze
@@ -283,9 +273,7 @@
          #f "[^A-Za-z0-9:]"
          (field GenoFreeze Name)
          'pre "_" 'post)
-        'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
+        'pre "_" 'post))
     (set xkos:classifiedUnder 'gnc:Genotype)
     (set rdfs:label (field GenoFreeze Name))
     (set dct:title (field GenoFreeze FullName))
@@ -295,9 +283,7 @@
                       '^^xsd:date))
     (set xkos:classifiedUnder
          (string->identifier
-            "set" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first))))
+            "set" (field InbredSet Name)))))
 
 ;; Molecular Traits are also referred to as ProbeSets
 (define-transformer probesetfreeze
@@ -319,9 +305,7 @@
        (regexp-substitute/global
         #f "[^A-Za-z0-9:]"
         (field ProbeSetFreeze Name)
-        'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
+        'pre "_" 'post))
     (set xkos:classifiedUnder 'gnc:Probeset)
     (set gnt:usesNormalization
          (string->identifier "avgMethod"
@@ -342,9 +326,7 @@
           (field Tissue Short_Name)))
     (set xkos:classifiedUnder
          (string->identifier
-          "set" (field InbredSet Name)
-          #:separator ""
-          #:proc string-capitalize-first))))
+          "set" (field InbredSet Name)))))
 
 
 
diff --git a/examples/strains.scm b/examples/strains.scm
index 44a0e87..5ef6f03 100755
--- a/examples/strains.scm
+++ b/examples/strains.scm
@@ -76,14 +76,10 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
             (regexp-substitute/global
              #f "[^A-Za-z0-9:]"
              (field Strain Name)
-             'pre "_" 'post)
-            #:separator ""
-            #:proc string-capitalize-first)
+             'pre "_" 'post))
     (set rdf:type 'gnc:strain)
     (set xkos:classifiedUnder
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                             #:separator ""
-                             #:proc string-capitalize-first))
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
     ;; Name, and maybe a second name
     (set rdfs:label (sanitize-rdf-string (field Strain Name)))
     (set skos:altLabel (sanitize-rdf-string (field ("IF ((Strain.Name2 != Strain.Name), Strain.Name2, '')" Name2))))
@@ -140,7 +136,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
       ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
       ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
    (inputs
-    (list inbred-set species strain mapping-method avg-method))
+    (list strain mapping-method avg-method))
    (outputs
     `(#:documentation ,documentation
       #:rdf ,output))))
diff --git a/transform/triples.scm b/transform/triples.scm
index 926b8a2..9775d36 100644
--- a/transform/triples.scm
+++ b/transform/triples.scm
@@ -23,11 +23,12 @@
         (string->symbol
          (format #f "~s~a" string-field schema)))))
 
-(define* (string->identifier prefix str
-                             #:optional #:key
-                             (ontology "gn:")
-                             (separator "_")
-                             (proc string-downcase))
+(define* (string->identifier
+          prefix str
+          #:optional #:key
+          (ontology "gn:")
+          (separator "")
+          (proc string-capitalize-first))
   "Convert STR to a turtle identifier after replacing illegal
 characters with an underscore and prefixing with gn:PREFIX."
   (if (or (and (string? str) (string-null? str))