Rename define-dump -> define-transformer

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

10 files changed, 25 insertions, 25 deletions

diff --git a/dump/special-forms.scm b/dump/special-forms.scm
index 7b32785..f771cc1 100644
--- a/dump/special-forms.scm
+++ b/dump/special-forms.scm
@@ -19,7 +19,7 @@
             blank-node
             map-alist
 	    dump-with-documentation
-            define-dump))
+            define-transformer))
 
 (define (key->assoc-ref alist x)
   "Recursively translate (key k) forms in source X to (assoc-ref ALIST
@@ -342,14 +342,14 @@ literals is optional. So,
         (syntax-let (bindings ...)
           body ...))))))
 
-(define-syntax define-dump
+(define-syntax define-transformer
   (lambda (x)
     "Define FUNCTION-NAME, a function that dumps a view of the database.
 
-define-dump consists of three order-agnostic clauses---tables,
+define-transformer consists of three order-agnostic clauses---tables,
 schema-triples and triples---in the form shown below.
 
-(define-dump function-name
+(define-transformer function-name
   (tables (table ...) raw-forms ...)
   (schema-triples
    (subject predicate object) ...)
@@ -537,7 +537,7 @@ The above query results to triples that have the form:
                                            (primary-table other-tables ...)
                                            tables-raw ...)))
              )))
-      (_ (error "Invalid define-dump syntax:" (syntax->datum x))))))
+      (_ (error "Invalid define-transformer syntax:" (syntax->datum x))))))
 
 (define (get-keyword-value args keyword default)
   (let ((kv (memq keyword args)))
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index a127e57..6173201 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -34,7 +34,7 @@
                        (list first-name last-name (fix-email-id email))
                        "_")))
 
-(define-dump dump-investigators
+(define-transformer dump-investigators
   ;; There are a few duplicate entries. We group by email to
   ;; deduplicate.
   (tables (Investigators)
@@ -56,7 +56,7 @@
     (set v:postal-code (field Investigators ZipCode))
     (set v:country-name (field Investigators Country))))
 
-(define-dump dump-gene-chip
+(define-transformer dump-gene-chip
   (tables (GeneChip
            (left-join Species "USING (SpeciesId)")))
   (schema-triples
@@ -87,7 +87,7 @@
          (ontology 'geoSeries:
                    (string-trim-both (field GeneChip GeoPlatform))))))
 
-(define-dump dump-info-files
+(define-transformer dump-info-files
   (tables (InfoFiles
            (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
            (left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name")
@@ -251,7 +251,7 @@
                                  (field Datasets Acknowledgment)))))
 
 ;; These are phenotype datasets that don't have Infofile metadata
-(define-dump dump-publishfreeze
+(define-transformer dump-publishfreeze
   (tables (PublishFreeze
            (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
            (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
@@ -277,7 +277,7 @@
           #:separator ""
           #:proc string-capitalize-first))))
 
-(define-dump dump-genofreeze
+(define-transformer dump-genofreeze
   (tables (GenoFreeze
            (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
            (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
@@ -308,7 +308,7 @@
             #:proc string-capitalize-first))))
 
 ;; Molecular Traits are also referred to as ProbeSets
-(define-dump dump-probesetfreeze
+(define-transformer dump-probesetfreeze
   (tables (ProbeSetFreeze
            (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
            (left-join ProbeFreeze "USING (ProbeFreezeId)")
diff --git a/examples/dump-generif.scm b/examples/dump-generif.scm
index 0689f57..f754274 100755
--- a/examples/dump-generif.scm
+++ b/examples/dump-generif.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-dump dump-genewiki-symbols
+(define-transformer dump-genewiki-symbols
   (tables (GeneRIF_BASIC
            (left-join Species "USING (SpeciesId)"))
           "GROUP BY GeneId ORDER BY BINARY symbol")
@@ -37,7 +37,7 @@
                             (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
                                           #\,)))))
 
-(define-dump dump-gn-genewiki-entries
+(define-transformer dump-gn-genewiki-entries
   (tables (GeneRIF
            (left-join GeneRIF_BASIC "USING (symbol)")
            (left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId")
@@ -101,7 +101,7 @@
                   (cut string-split-substring <> "::::")
                   comments))))))
 
-(define-dump dump-ncbi-genewiki-entries
+(define-transformer dump-ncbi-genewiki-entries
   (tables (GeneRIF_BASIC)
           "GROUP BY GeneId, comment, createtime")
   (schema-triples
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 30e7796..a055039 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -30,7 +30,7 @@
     ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
     [str str]))
 
-(define-dump dump-genotypes
+(define-transformer dump-genotypes
   (tables (Geno
            (left-join Species "USING (SpeciesId)")))
   (schema-triples
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index abcf140..b7ae003 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -19,7 +19,7 @@
     read))
 
 
-(define-dump dump-phenotypes
+(define-transformer dump-phenotypes
   (tables (PublishXRef
            (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
            (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
diff --git a/examples/dump-probeset-data.scm b/examples/dump-probeset-data.scm
index 54615bc..55f3f4b 100755
--- a/examples/dump-probeset-data.scm
+++ b/examples/dump-probeset-data.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-dump dump-probeset-data
+(define-transformer dump-probeset-data
   (tables (ProbeSetXRef
            (left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
            (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"))
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index c614a76..3a55506 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -17,7 +17,7 @@
     read))
 
 
-(define-dump dump-probeset
+(define-transformer dump-probeset
   (tables (ProbeSet
            (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
   (schema-triples
diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm
index 5b1af83..1881872 100755
--- a/examples/dump-publication.scm
+++ b/examples/dump-publication.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-dump dump-publication
+(define-transformer dump-publication
   (tables (Publication))
   (triples
       (let ((pmid (field
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
index 20b0b05..b0ac6f8 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/dump-species-metadata.scm
@@ -28,7 +28,7 @@
     ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
     [str str]))
 
-(define-dump dump-species
+(define-transformer dump-species
   (tables (Species))
   (schema-triples
    (gnc:species a skos:Concept)
@@ -97,7 +97,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
 
 !#
 
-(define-dump dump-strain
+(define-transformer dump-strain
   (tables (Strain
            (left-join Species "ON Strain.SpeciesId = Species.SpeciesId")))
   (schema-triples
@@ -129,7 +129,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
     (set gnt:alias (sanitize-rdf-string (field ("IF ((Strain.Alias != Strain.Name), Strain.Alias, '')" Alias))))
     (set gnt:symbol (field ("IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '')" Symbol)))))
 
-(define-dump dump-mapping-method
+(define-transformer dump-mapping-method
   (tables (MappingMethod))
   (schema-triples
    (gnc:mappingMethod a skos:Concept)
@@ -140,7 +140,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
     (set rdfs:label (field MappingMethod Name))))
 
 
-(define-dump dump-inbred-set
+(define-transformer dump-inbred-set
   (tables (InbredSet
            (left-join Species "ON InbredSet.SpeciesId=Species.Id")
            (left-join MappingMethod
@@ -189,7 +189,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
                         molecularTrait))
                 "||")))))
 
-(define-dump dump-avg-method
+(define-transformer dump-avg-method
   ;; The Name and Normalization fields seem to be the same. Dump only
   ;; the Name field.
   (tables (AvgMethod))
diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm
index f11b8b4..3658a26 100755
--- a/examples/dump-tissue.scm
+++ b/examples/dump-tissue.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-dump dump-tissue
+(define-transformer dump-tissue
     ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
     ;; and BIRN_lex_Name are mostly NULL.
     (tables (Tissue))