Rename dump -> transform

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

19 files changed, 82 insertions, 82 deletions

diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
index 5680a2b..783b2b7 100755
--- a/examples/dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -5,10 +5,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
diff --git a/examples/generif.scm b/examples/generif.scm
index 0b3c8e4..76f55ee 100755
--- a/examples/generif.scm
+++ b/examples/generif.scm
@@ -5,10 +5,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
@@ -64,7 +64,7 @@
              'gn:geneWikiEntry))
     (set gnt:wikiEntryOfSpecies
          (string->binomial-name (field Species FullName)))
-    ;; This only dumps symbols not present in the GeneRIF_BASIC table
+    ;; This only transforms symbols not present in the GeneRIF_BASIC table
     (set gnt:symbol (let ([geneid (field GeneRIF_BASIC GeneId)])
                      (if (eq? geneid 0)
                          (field GeneRIF symbol)
diff --git a/examples/genotype.scm b/examples/genotype.scm
index 63b85a7..6fe60c9 100755
--- a/examples/genotype.scm
+++ b/examples/genotype.scm
@@ -7,10 +7,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
@@ -86,7 +86,7 @@
                          '^^xsd:double))
     (set gnt:hasSequence (field Geno Sequence))
     (set gnt:hasSource (field Geno Source))
-    ;; Only dump Source2 if it differs from Source
+    ;; Only transform Source2 if it differs from Source
     (set gnt:hasAltSourceName
          (field ("IF((Source2 = Source), NULL, Source2)"
                  Source2)))
diff --git a/examples/phenotype.scm b/examples/phenotype.scm
index 1c68159..31d7972 100755
--- a/examples/phenotype.scm
+++ b/examples/phenotype.scm
@@ -7,10 +7,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
diff --git a/examples/probeset-data.scm b/examples/probeset-data.scm
index d46bcda..ebb6a92 100755
--- a/examples/probeset-data.scm
+++ b/examples/probeset-data.scm
@@ -5,10 +5,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
diff --git a/examples/probeset.scm b/examples/probeset.scm
index 68ddb59..2dfdbc2 100755
--- a/examples/probeset.scm
+++ b/examples/probeset.scm
@@ -5,10 +5,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
diff --git a/examples/publication.scm b/examples/publication.scm
index 313ee96..d9e2aa5 100755
--- a/examples/publication.scm
+++ b/examples/publication.scm
@@ -5,10 +5,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
diff --git a/examples/species-metadata.scm b/examples/species-metadata.scm
index f3794b8..b67c0bc 100755
--- a/examples/species-metadata.scm
+++ b/examples/species-metadata.scm
@@ -5,10 +5,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
diff --git a/examples/tissue.scm b/examples/tissue.scm
index 8ce96c8..22b715e 100755
--- a/examples/tissue.scm
+++ b/examples/tissue.scm
@@ -5,10 +5,10 @@
              (srfi srfi-26)
              (ice-9 match)
              (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
 
 
 
diff --git a/json-dump.scm b/json-dump.scm
index 8625139..0a054c5 100755
--- a/json-dump.scm
+++ b/json-dump.scm
@@ -4,7 +4,7 @@
 (use-modules (json)
              (ice-9 ftw)
              (ice-9 match)
-             (dump triples))
+             (transform triples))
 
 
 
diff --git a/tests.scm b/tests.scm
index 7ba4261..1dfa2ac 100644
--- a/tests.scm
+++ b/tests.scm
@@ -1,9 +1,9 @@
 (use-modules (srfi srfi-64)
              (ice-9 match)
-             (dump sql)
-             (dump string-similarity)
-             (dump strings)
-             (dump special-forms))
+             (transform sql)
+             (transform string-similarity)
+             (transform strings)
+             (transform special-forms))
 
 (test-begin "sql")
 
@@ -24,23 +24,23 @@
 
 (test-equal "trigrams of a string"
   (list "coe" "oef" "eff" "ffi" "fic" "ici" "cie" "ien" "ent")
-  ((@@ (dump string-similarity) trigrams) "coefficient"))
+  ((@@ (transform string-similarity) trigrams) "coefficient"))
 
 (test-equal "Jaccard index"
   0.4
-  ((@@ (dump string-similarity) jaccard-index)
+  ((@@ (transform string-similarity) jaccard-index)
    (list 0 1 2 5 6 8 9)
    (list 0 2 3 4 5 7 9)))
 
 (test-equal "Jaccard index of equal sets"
   1.0
-  ((@@ (dump string-similarity) jaccard-index)
+  ((@@ (transform string-similarity) jaccard-index)
    (iota 10)
    (iota 10)))
 
 (test-equal "Jaccard index of disjoint sets"
   0.0
-  ((@@ (dump string-similarity) jaccard-index)
+  ((@@ (transform string-similarity) jaccard-index)
    (iota 10)
    (iota 10 10)))
 
diff --git a/dump/schema-dump.scm b/transform/schema-dump.scm
index 525bf65..bf7f8cb 100644
--- a/dump/schema-dump.scm
+++ b/transform/schema-dump.scm
@@ -1,10 +1,10 @@
-(define-module (dump schema)
+(define-module (transform schema)
   #:use-module (ice-9 match)
   #:use-module (ice-9 srfi-26)
-  #:use-module (dump sql)
-  #:use-module (dump triples)
-  #:use-module (dump strings)
-  #:use-module (dump table))
+  #:use-module (transform sql)
+  #:use-module (transform triples)
+  #:use-module (transform strings)
+  #:use-module (transform table))
 
 
 (define (table-fields db table)
diff --git a/dump/special-forms.scm b/transform/special-forms.scm
index 2650580..4b69337 100644
--- a/dump/special-forms.scm
+++ b/transform/special-forms.scm
@@ -1,10 +1,10 @@
-(define-module (dump special-forms)
+(define-module (transform special-forms)
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-26)
-  #:use-module (dump sql)
-  #:use-module (dump table)
-  #:use-module (dump triples)
+  #:use-module (transform sql)
+  #:use-module (transform table)
+  #:use-module (transform triples)
   #:export (translate-forms
             collect-forms
             collect-keys
@@ -279,7 +279,7 @@ ALIST field-name) forms."
   (define (id table predicate)
     (symbol->string
      (string->identifier
-      "dump"
+      "transform"
       (string-append
        table "_" (remove-namespace (symbol->string predicate)))))))
 
@@ -344,7 +344,7 @@ literals is optional. So,
 
 (define-syntax define-transformer
   (lambda (x)
-    "Define FUNCTION-NAME, a function that dumps a view of the database.
+    "Define FUNCTION-NAME, a function that transforms a view of the database.
 
 define-transformer consists of three order-agnostic clauses---tables,
 schema-triples and triples---in the form shown below.
@@ -357,7 +357,7 @@ schema-triples and triples---in the form shown below.
     (verb predicate object) ...))
 
 The tables clause specifies the database tables to be joined to
-construct the view to be dumped. TABLE must be either of the form
+construct the view to be transformed. TABLE must be either of the form
 TABLE-NAME or of the form (JOIN-OPERATOR TABLE-NAME
 RAW-CONDITION). TABLE-NAME must, obviously, be the name of the
 table. JOIN-OPERATOR must be one of join, left-join and
@@ -367,9 +367,9 @@ string. This is usually something like
 strings to be appended to the SQL query.
 
 The schema-triples clause specifies the list of triples to be written
-once when the dump starts.
+once when the transform starts.
 
-The triples clause specifies the triples to be dumped once for each
+The triples clause specifies the triples to be transformed once for each
 row in the view. All triples have a common SUBJECT. The (verb
 predicate object) clauses are described below.
 
@@ -409,11 +409,11 @@ must be remedied."
                     (map (lambda (predicate-clause)
                            (syntax-case predicate-clause ()
                              ((_ predicate _)
-                              ;; Dump metadata about the dump itself.
+                              ;; Dump metadata about the transform itself.
                               #`(begin
                                   (scm->triples
                                    (map-alist '()
-	        		     (set rdf:type 'gn-id:dump)
+	        		     (set rdf:type 'gn-id:transform)
 	        		     (set gn-term:createsPredicate 'predicate)
 	        		     (filter-set gn-term:forSubjectType #,subject-type)
 	        		     (multiset gn-term:dependsOn
diff --git a/dump/sql.scm b/transform/sql.scm
index 9e6b21a..a8962c8 100644
--- a/dump/sql.scm
+++ b/transform/sql.scm
@@ -3,7 +3,7 @@
 ;;; Most of these functions should have been a part of
 ;;; guile-dbi. Never too late to contribute upstream!
 
-(define-module (dump sql)
+(define-module (transform sql)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
diff --git a/dump/string-similarity.scm b/transform/string-similarity.scm
index 4bcdf7c..c715856 100644
--- a/dump/string-similarity.scm
+++ b/transform/string-similarity.scm
@@ -1,4 +1,4 @@
-(define-module (dump string-similarity)
+(define-module (transform string-similarity)
   #:use-module (srfi srfi-1)
   #:export (jaccard-string-similar?))
 
diff --git a/dump/strings.scm b/transform/strings.scm
index e965f03..98f828f 100644
--- a/dump/strings.scm
+++ b/transform/strings.scm
@@ -1,4 +1,4 @@
-(define-module (dump strings)
+(define-module (transform strings)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-19)
   #:use-module (ice-9 match)
diff --git a/dump/table.scm b/transform/table.scm
index 834c4fd..e6254d0 100644
--- a/dump/table.scm
+++ b/transform/table.scm
@@ -1,4 +1,4 @@
-(define-module (dump table)
+(define-module (transform table)
   #:use-module (srfi srfi-9 gnu)
   #:export (make-table
             table-name
@@ -8,7 +8,7 @@
             make-column
             column-name
             column-type
-            column-dumped?))
+            column-transformed?))
 
 (define-immutable-record-type <table>
   (make-table name size columns)
@@ -18,11 +18,11 @@
   (columns table-columns set-table-columns))
 
 (define-immutable-record-type <column>
-  (column-constructor name type dumped?)
+  (column-constructor name type transformed?)
   column?
   (name column-name)
   (type column-type)
-  (dumped? column-dumped?))
+  (transformed? column-transformed?))
 
-(define* (make-column name type #:optional dumped?)
-  (column-constructor name type dumped?))
+(define* (make-column name type #:optional transformed?)
+  (column-constructor name type transformed?))
diff --git a/dump/triples.scm b/transform/triples.scm
index b0eb1e4..8a64c5b 100644
--- a/dump/triples.scm
+++ b/transform/triples.scm
@@ -1,7 +1,7 @@
-(define-module (dump triples)
+(define-module (transform triples)
   #:use-module (ice-9 regex)
   #:use-module (ice-9 match)
-  #:use-module (dump strings)
+  #:use-module (transform strings)
   #:export (ontology
             string->identifier
             prefix
diff --git a/visualize-schema.scm b/visualize-schema.scm
index 6850cb8..92f9272 100755
--- a/visualize-schema.scm
+++ b/visualize-schema.scm
@@ -12,8 +12,8 @@
              (sparql driver)
              (sparql lang)
              (sparql util)
-             (dump string-similarity)
-             (dump table))
+             (transform string-similarity)
+             (transform table))
 
 (define rdfs
   (prefix "http://www.w3.org/2000/01/rdf-schema#"))
@@ -83,7 +83,7 @@
   "Return HTML string label for TABLE."
   (sxml->graphviz-html
    `(table (@ (cellborder 0)
-              (bgcolor ,(if (any column-dumped?
+              (bgcolor ,(if (any column-transformed?
                                  (table-columns table))
                             "lightgrey"
                             "white")))
@@ -94,7 +94,7 @@
                             (human-units (table-size table)))))
            ,@(map (lambda (column)
                     `(tr (td (@ (port ,(column-name column))
-                                ,@(if (column-dumped? column)
+                                ,@(if (column-transformed? column)
                                       `((bgcolor "green"))
                                       '()))
                              ,(column-name column))))
@@ -140,17 +140,17 @@ return #f. ALL-TABLES is a list of all tables in the database."
   "Return list of all tables in DB. Each element of the returned list
 is a <table> object."
   (map (match-lambda
-         ((table size fields field-types field-dumped)
+         ((table size fields field-types field-transformed)
           (make-table table
                       (string->number size)
                       (map make-column
                            (string-split fields #\,)
                            (string-split field-types #\,)
                            (map (cut string=? <> "1")
-                                (string-split field-dumped #\,))))))
+                                (string-split field-transformed #\,))))))
        (sparql-query-records
         "PREFIX gn: <http://genenetwork.org/>
-SELECT SAMPLE(?tablename) SAMPLE(?size) GROUP_CONCAT(?fieldname ; separator=\",\") GROUP_CONCAT(?fieldtype ; separator=\",\") GROUP_CONCAT(EXISTS{ ?dump rdf:type gn:dump . ?dump gn:dependsOn ?field .} ; separator=\",\")
+SELECT SAMPLE(?tablename) SAMPLE(?size) GROUP_CONCAT(?fieldname ; separator=\",\") GROUP_CONCAT(?fieldtype ; separator=\",\") GROUP_CONCAT(EXISTS{ ?transform rdf:type gn:transform . ?transform gn:dependsOn ?field .} ; separator=\",\")
 WHERE
 {
   ?table rdf:type gn:sqlTable ;
@@ -239,7 +239,7 @@ WHERE
 {
   ?predicate rdfs:domain ?type ;
              rdfs:range rdfs:Literal .
-  ?dump rdf:type gn:dump ;
+  ?transform rdf:type gn:transform ;
         gn:createsPredicate ?predicate ;
         gn:forSubjectType ?type ;
         gn:dependsOn ?field .