Remove "dump-" prefix

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

9 files changed, 69 insertions, 77 deletions

diff --git a/examples/dump-dataset-metadata.scm b/examples/dataset-metadata.scm
index 6173201..5680a2b 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -34,7 +34,7 @@
                        (list first-name last-name (fix-email-id email))
                        "_")))
 
-(define-transformer dump-investigators
+(define-transformer 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-transformer dump-gene-chip
+(define-transformer gene-chip
   (tables (GeneChip
            (left-join Species "USING (SpeciesId)")))
   (schema-triples
@@ -87,7 +87,7 @@
          (ontology 'geoSeries:
                    (string-trim-both (field GeneChip GeoPlatform))))))
 
-(define-transformer dump-info-files
+(define-transformer 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-transformer dump-publishfreeze
+(define-transformer 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-transformer dump-genofreeze
+(define-transformer 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-transformer dump-probesetfreeze
+(define-transformer probesetfreeze
   (tables (ProbeSetFreeze
            (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
            (left-join ProbeFreeze "USING (ProbeFreezeId)")
@@ -356,7 +356,7 @@
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "Info files / Investigators Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -375,13 +375,13 @@
     ("taxon:" "<http://purl.uniprot.org/taxonomy/>")
     ("dct:" "<http://purl.org/dc/terms/>")))
  (inputs
-  (list dump-info-files
-        dump-publishfreeze
-        dump-genofreeze
-        dump-probesetfreeze
-        dump-investigators
-        dump-gene-chip))
+  (list info-files
+        publishfreeze
+        genofreeze
+        probesetfreeze
+        investigators
+        gene-chip))
  (outputs
-  '(#:documentation "./docs/dump-info-pages.md"
-    #:rdf "/export/data/genenetwork-virtuoso/dump-info-pages.ttl")))
+  '(#:documentation "./docs/info-pages.md"
+    #:rdf "/export/data/genenetwork-virtuoso/info-pages.ttl")))
 
diff --git a/examples/dump-generif.scm b/examples/generif.scm
index f754274..0b3c8e4 100755
--- a/examples/dump-generif.scm
+++ b/examples/generif.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-transformer dump-genewiki-symbols
+(define-transformer 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-transformer dump-gn-genewiki-entries
+(define-transformer 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-transformer dump-ncbi-genewiki-entries
+(define-transformer ncbi-genewiki-entries
   (tables (GeneRIF_BASIC)
           "GROUP BY GeneId, comment, createtime")
   (schema-triples
@@ -124,7 +124,7 @@
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "GeneRIF Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -141,10 +141,10 @@
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
     ("owl:" "<http://www.w3.org/2002/07/owl#>")))
  (inputs
-  (list ;; dump-genewiki-symbols
-        dump-gn-genewiki-entries
-        ;; dump-ncbi-genewiki-entries
+  (list ;; genewiki-symbols
+        gn-genewiki-entries
+        ;; ncbi-genewiki-entries
         ))
  (outputs
-   '(#:documentation "./docs/dump-generif.md"
-     #:rdf "./verified-data/dump-generif.ttl")))
+   '(#:documentation "./docs/generif.md"
+     #:rdf "./verified-data/generif.ttl")))
diff --git a/examples/dump-genotype.scm b/examples/genotype.scm
index a055039..63b85a7 100755
--- a/examples/dump-genotype.scm
+++ b/examples/genotype.scm
@@ -30,7 +30,7 @@
     ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
     [str str]))
 
-(define-transformer dump-genotypes
+(define-transformer genotypes
   (tables (Geno
            (left-join Species "USING (SpeciesId)")))
   (schema-triples
@@ -103,7 +103,7 @@
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "Genotype Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -118,7 +118,7 @@
     ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
  (inputs
-  (list dump-genotypes))
+  (list genotypes))
  (outputs
-  '(#:documentation "./docs/dump-genotype.md"
-    #:rdf "/export/data/genenetwork-virtuoso/dump-genotype.ttl")))
+  '(#:documentation "./docs/genotype.md"
+    #:rdf "/export/data/genenetwork-virtuoso/genotype.ttl")))
diff --git a/examples/dump-phenotype.scm b/examples/phenotype.scm
index b7ae003..1c68159 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/phenotype.scm
@@ -19,7 +19,7 @@
     read))
 
 
-(define-transformer dump-phenotypes
+(define-transformer phenotypes
   (tables (PublishXRef
            (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
            (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
@@ -102,7 +102,7 @@
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "Phenotypes Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -119,7 +119,7 @@
     ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
  (inputs
   (list
-   dump-phenotypes))
+   phenotypes))
  (outputs
-  '(#:documentation "./docs/dump-phenotype.md"
-    #:rdf "/export/data/genenetwork-virtuoso/dump-phenotype.ttl")))
+  '(#:documentation "./docs/phenotype.md"
+    #:rdf "/export/data/genenetwork-virtuoso/phenotype.ttl")))
diff --git a/examples/dump-probeset-data.scm b/examples/probeset-data.scm
index 55f3f4b..d46bcda 100755
--- a/examples/dump-probeset-data.scm
+++ b/examples/probeset-data.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-transformer dump-probeset-data
+(define-transformer probeset-data
   (tables (ProbeSetXRef
            (left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
            (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"))
@@ -74,19 +74,11 @@
     (set gnt:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
                                     '^^xsd:double))
     (set gnt:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
-                                '^^xsd:double))
-    (set gnt:belongsToDataset
-         (string->identifier
-          ""
-          (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                    (field ProbeSetFreeze Name)
-                                    'pre "_" 'post)
-          #:separator ""
-          #:proc string-capitalize-first))))
+                                '^^xsd:double))))
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "Probeset Summary Statistics")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -100,7 +92,7 @@
     ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
  (inputs
-  (list dump-probeset-data))
+  (list probeset-data))
  (outputs
-  '(#:documentation "./docs/dump-probeset-summary-stats.md"
-    #:rdf "./verified-data/dump-probeset-summary-stats.ttl")))
+  '(#:documentation "./docs/probeset-summary-stats.md"
+    #:rdf "./verified-data/probeset-summary-stats.ttl")))
diff --git a/examples/dump-probeset.scm b/examples/probeset.scm
index 3a55506..68ddb59 100755
--- a/examples/dump-probeset.scm
+++ b/examples/probeset.scm
@@ -17,7 +17,7 @@
     read))
 
 
-(define-transformer dump-probeset
+(define-transformer probeset
   (tables (ProbeSet
            (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
   (schema-triples
@@ -156,7 +156,7 @@
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "ProbeSet Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -178,7 +178,7 @@
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
     ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
  (inputs
-  (list dump-probeset))
+  (list probeset))
  (outputs
-  '(#:documentation "./docs/dump-probeset.md"
-    #:rdf "./verified-data/dump-probeset.ttl")))
+  '(#:documentation "./docs/probeset.md"
+    #:rdf "./verified-data/probeset.ttl")))
diff --git a/examples/dump-publication.scm b/examples/publication.scm
index 1881872..313ee96 100755
--- a/examples/dump-publication.scm
+++ b/examples/publication.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-transformer dump-publication
+(define-transformer publication
   (tables (Publication))
   (triples
       (let ((pmid (field
@@ -59,7 +59,7 @@
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "Publications Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -75,7 +75,7 @@
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
     ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")))
  (inputs
-  (list dump-publication))
+  (list publication))
  (outputs
-  '(#:documentation "./docs/dump-publication.md"
-    #:rdf "./verified-data/dump-publication.ttl")))
+  '(#:documentation "./docs/publication.md"
+    #:rdf "./verified-data/publication.ttl")))
diff --git a/examples/dump-species-metadata.scm b/examples/species-metadata.scm
index b0ac6f8..f3794b8 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/species-metadata.scm
@@ -28,7 +28,7 @@
     ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
     [str str]))
 
-(define-transformer dump-species
+(define-transformer 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-transformer dump-strain
+(define-transformer 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-transformer dump-mapping-method
+(define-transformer 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-transformer dump-inbred-set
+(define-transformer inbred-set
   (tables (InbredSet
            (left-join Species "ON InbredSet.SpeciesId=Species.Id")
            (left-join MappingMethod
@@ -152,7 +152,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
    (gnt:geneticType rdfs:domain gnc:set)
    (gnt:code a owl:ObjectProperty)
    (gnt:code rdfs:domain gnc:set)
-   ;; Already defined as an owl prop in dump-species
+   ;; Already defined as an owl prop in species
    (gnt:family rdfs:domain gnc:set)
    (gnt:phenotype a owl:ObjectProperty)
    (gnt:phenotype rdfs:domain gnc:set)
@@ -189,7 +189,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
                         molecularTrait))
                 "||")))))
 
-(define-transformer dump-avg-method
+(define-transformer avg-method
   ;; The Name and Normalization fields seem to be the same. Dump only
   ;; the Name field.
   (tables (AvgMethod))
@@ -201,7 +201,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "Species Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -216,11 +216,11 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
     ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
  (inputs
   (list
-   dump-inbred-set
-   dump-species
-   dump-strain
-   dump-mapping-method
-   dump-avg-method))
+   inbred-set
+   species
+   strain
+   mapping-method
+   avg-method))
  (outputs
-  '(#:documentation "./docs/dump-species-metadata.md"
-    #:rdf "/export/data/genenetwork-virtuoso/dump-species-metadata.ttl")))
+  '(#:documentation "./docs/species-metadata.md"
+    #:rdf "/export/data/genenetwork-virtuoso/species-metadata.ttl")))
diff --git a/examples/dump-tissue.scm b/examples/tissue.scm
index 3658a26..8ce96c8 100755
--- a/examples/dump-tissue.scm
+++ b/examples/tissue.scm
@@ -18,7 +18,7 @@
 
 
 
-(define-transformer dump-tissue
+(define-transformer tissue
     ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
     ;; and BIRN_lex_Name are mostly NULL.
     (tables (Tissue))
@@ -32,7 +32,7 @@
 
 
 
-(dump-with-documentation
+(with-documentation
  (name "Tissue Metadata")
  (connection %connection-settings)
  (table-metadata? #f)
@@ -44,7 +44,7 @@
     ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
     ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
  (inputs
-  (list dump-tissue))
+  (list tissue))
  (outputs
-  '(#:documentation "./docs/dump-tissue.md"
-    #:rdf "./verified-data/dump-tissue.ttl")))
+  '(#:documentation "./docs/tissue.md"
+    #:rdf "./verified-data/tissue.ttl")))