Remove "dump-" prefix

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

12 files changed, 101 insertions, 109 deletions

diff --git a/dump/schema-dump.scm b/dump/schema-dump.scm
index 86626f4..525bf65 100644
--- a/dump/schema-dump.scm
+++ b/dump/schema-dump.scm
@@ -7,7 +7,7 @@
   #:use-module (dump table))
 
 
-(define (dump-table-fields db table)
+(define (table-fields db table)
   (format #t "* ~a~%" table)
   (match (sql-find db
                    (select-query ((TableComments Comment))
@@ -41,10 +41,10 @@
            (select-query ((TableComments TableName))
                          (TableComments))))
 
-(define (dump-schema-annotations db)
+(define (schema-annotations db)
   (call-with-target-database
    (lambda (db)
-     (for-each (cut dump-table-fields db <>)
+     (for-each (cut table-fields db <>)
                (get-tables-from-comments db)))))
 
 (define (tables db)
@@ -70,7 +70,7 @@ is a <table> object."
                               (format #f "WHERE table_schema = '~a'"
                                       (assq-ref %connection-settings 'sql-database))))))
 
-(define (dump-schema db)
+(define (schema db)
   (let ((tables (tables db)))
     (for-each (lambda (table)
                 (let ((table-id (string->identifier
@@ -94,13 +94,13 @@ is a <table> object."
                             (table-columns table))))
               tables)))
 
-(define* (dump-data-table db table-name data-field
-                          #:optional (default-dump-directory ""))
-  (let ((dump-directory (string-append default-dump-directory "/" table-name))
+(define* (data-table db table-name data-field
+                          #:optional (default-directory ""))
+  (let ((directory (string-append default-directory "/" table-name))
         (port #f)
         (current-strain-id #f))
-    (unless (file-exists? dump-directory)
-      (mkdir dump-directory))
+    (unless (file-exists? directory)
+      (mkdir directory))
     (sql-for-each (match-lambda
                     (((_ . strain-id)
                       (_ . value))
@@ -112,7 +112,7 @@ is a <table> object."
                      ;; If no file is open, open new file.
                      (unless port
                        (set! current-strain-id strain-id)
-                       (let ((filename (string-append dump-directory
+                       (let ((filename (string-append directory
                                                       "/" (number->string strain-id))))
                          (display filename (current-error-port))
                          (newline (current-error-port))
diff --git a/dump/special-forms.scm b/dump/special-forms.scm
index f771cc1..2650580 100644
--- a/dump/special-forms.scm
+++ b/dump/special-forms.scm
@@ -14,11 +14,11 @@
             find-clause
             remove-namespace
             column-id
-            dump-id
+            id
             syntax-let
             blank-node
             map-alist
-	    dump-with-documentation
+	    with-documentation
             define-transformer))
 
 (define (key->assoc-ref alist x)
@@ -276,12 +276,12 @@ ALIST field-name) forms."
                   "user2" table-name)
               "__" column-name)))
 
-  (define (dump-id dump-table predicate)
+  (define (id table predicate)
     (symbol->string
      (string->identifier
       "dump"
       (string-append
-       dump-table "_" (remove-namespace (symbol->string predicate)))))))
+       table "_" (remove-namespace (symbol->string predicate)))))))
 
 (define-syntax blank-node
   (syntax-rules ()
@@ -396,11 +396,11 @@ must be remedied."
                     ((triples subject predicate-clauses ...) (triples)
                      (find-clause #'(clauses ...) 'triples)))
          #`(define* (name db #:key
-                          (dump-metadata? #f)
-                          (dump-data? #t)
-                          (dump-documentation? #f))
-             (when dump-metadata?
-               #,@(let ((dump-table (symbol->string (syntax->datum #'primary-table)))
+                          (metadata? #f)
+                          (data? #t)
+                          (documentation? #f))
+             (when metadata?
+               #,@(let ((table (symbol->string (syntax->datum #'primary-table)))
                         (subject-type (any (lambda (predicate)
                                              (syntax-case predicate (rdf:type)
                                                ((_ rdf:type type) #'type)
@@ -427,14 +427,14 @@ must be remedied."
 	        					    (datum->syntax
 	        					     x (column-id query (symbol->string alias))))))
 	        				       (collect-fields predicate-clause))))
-                                   #,(dump-id dump-table (syntax->datum #'predicate)))
+                                   #,(id table (syntax->datum #'predicate)))
                                   ;; Automatically create domain triples
                                   ;; for predicates.
                                   (when #,subject-type
                                     (triple 'predicate 'rdfs:domain #,subject-type))))
                              (_ (error "Invalid predicate clause:" predicate-clause))))
                          #'(predicate-clauses ...))))
-             (when dump-documentation?
+             (when documentation?
                (format #t "~%## '~a'~%~%" (syntax->datum #'name))
                #,(syntax-case #'schema-triples-clause (schema-triples)
                    ((schema-triples (triple-subject triple-predicate triple-object) ...)
@@ -477,7 +477,7 @@ The above query results to triples that have the form:
                              '()
                            #,@(field->datum #'(predicate-clauses ...))))
                (format #t "```~%Here's an example query:~%~%```sparql~%")
-               (dump-documentation?)
+               (documentation?)
                (newline)
                (let* ((result
                        (map-alist (sql-find
@@ -520,7 +520,7 @@ The above query results to triples that have the form:
                                                    (primary-table other-tables ...)
                                                    tables-raw ...)))
                (format #t "```~%~%"))
-             (when dump-data?
+             (when data?
                #,(syntax-case #'schema-triples-clause (schema-triples)
                    ((schema-triples (triple-subject triple-predicate triple-object) ...)
                     #`(for-each triple
@@ -545,7 +545,7 @@ The above query results to triples that have the form:
         (cadr kv)
         default)))
 
-(define-syntax dump-with-documentation
+(define-syntax with-documentation
   (syntax-rules ()
     ((_ (key value) ...)
      (let* ((alist `((key . ,value) ...))
@@ -567,9 +567,9 @@ The above query results to triples that have the form:
               (for-each
                (lambda (proc)
                  (proc db
-                       #:dump-metadata? #f
-                       #:dump-data? #f
-                       #:dump-documentation?
+                       #:metadata? #f
+                       #:data? #f
+                       #:documentation?
                        (lambda () (for-each
                                    (match-lambda
                                      ((k v)
@@ -593,7 +593,7 @@ The above query results to triples that have the form:
               (newline)
               (for-each
                (lambda (proc)
-                 (proc db #:dump-metadata? table-metadata?))
+                 (proc db #:metadata? table-metadata?))
                inputs))
             #:encoding "UTF-8")))))))
 
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")))
diff --git a/json-dump.scm b/json-dump.scm
index ccb64bc..8625139 100755
--- a/json-dump.scm
+++ b/json-dump.scm
@@ -8,7 +8,7 @@
 
 
 
-(define %dump-directory
+(define %directory
   (list-ref (command-line) 2))
 
 (define %data-directory
@@ -55,9 +55,9 @@ inside it."
     result)
   (file-system-fold enter? leaf down up skip error 0 path))
 
-(define (dump-rdf path)
+(define (rdf path)
   (with-output-to-file
-      (string-append %dump-directory "/sampledata.ttl")
+      (string-append %directory "/sampledata.ttl")
     (lambda ()
       (prefix "gn:" "<http://genenetwork.org/>")
       (newline)
@@ -70,4 +70,4 @@ inside it."
                   (newline))
                 (json-metadata->rdf file))))))))
 
-(dump-rdf %data-directory)
+(rdf %data-directory)