Remove "dump-" prefix

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

1 files changed, 0 insertions, 150 deletions

diff --git a/examples/dump-generif.scm b/examples/dump-generif.scm
deleted file mode 100755
index f754274..0000000
--- a/examples/dump-generif.scm
+++ /dev/null
@@ -1,150 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-(use-modules (srfi srfi-1)
-             (srfi srfi-26)
-             (ice-9 match)
-             (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
-
-
-
-(define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
-
-
-(define-transformer dump-genewiki-symbols
-  (tables (GeneRIF_BASIC
-           (left-join Species "USING (SpeciesId)"))
-          "GROUP BY GeneId ORDER BY BINARY symbol")
-  (schema-triples
-   (gnt:symbol rdfs:domain gn-term:geneWikiEntry)
-   (gnt:wikiEntryOfSpecies rdfs:range gn:species)
-   (gnt:taxid rdfs:domain gn-term:geneWikiEntry))
-  (triples (ontology 'generif: (field GeneRIF_BASIC GeneId))
-    (multiset gnt:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol))
-                                      #\,))
-    (multiset gnt:wikiEntryOfSpecies
-              (string-split
-               (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species))
-               #\,))
-    (multiset gnt:taxId (map (cut ontology 'ncbiTaxon: <>)
-                            (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
-                                          #\,)))))
-
-(define-transformer dump-gn-genewiki-entries
-  (tables (GeneRIF
-           (left-join GeneRIF_BASIC "USING (symbol)")
-           (left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId")
-           (left-join GeneRIFXRef "ON GeneRIFXRef.GeneRIFId = GeneRIF.Id")
-           (left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id"))
-          "WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 GROUP BY GeneRIF.symbol")
-  (schema-triples
-   (gnt:geneWikiEntry a rdfs:Class)
-   (gnt:geneWikiEntry a owl:Class)
-   (gnt:geneWikiEntry rdfs:comment "Represents GeneRIF Entries")
-   (gnt:geneCategory rdfs:domain gn:geneWikiEntry)
-   (gnt:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry)
-   (gnt:geneWikiEntry rdfs:domain gn:geneWikiEntry))
-  (triples
-      (let ([geneid (field GeneRIF_BASIC GeneId)])
-        (if (eq? geneid 0)
-            (ontology 'gnt:anonSymbol_
-                      (field GeneRIF symbol))
-            (ontology 'generif:
-                      geneid)))
-    (set rdf:type
-         (if (string-null? (field ("IFNULL(GeneRIF_BASIC.GeneId, '')" geneWikiEntryP)))
-             ""
-             'gn:geneWikiEntry))
-    (set gnt:wikiEntryOfSpecies
-         (string->binomial-name (field Species FullName)))
-    ;; This only dumps symbols not present in the GeneRIF_BASIC table
-    (set gnt:symbol (let ([geneid (field GeneRIF_BASIC GeneId)])
-                     (if (eq? geneid 0)
-                         (field GeneRIF symbol)
-                         "")))
-    (multiset gnt:geneWikiEntryOfGn
-              (let* ([entries
-                      (sanitize-rdf-string
-                       (field
-                        ("GROUP_CONCAT(DISTINCT CONCAT_WS('::::', IFNULL(GeneCategory.Name, ''), IFNULL(GeneRIF.PubMed_ID, ''), GeneRIF.email, CAST(CONVERT(BINARY CONVERT(GeneRIF.comment USING latin1) USING utf8) AS VARCHAR(15000)), GeneRIF.createtime, IFNULL(weburl, '')) SEPARATOR';;;;;')"
-                         wikientry)))]
-                     [comments (string-split-substring entries ";;;;;")])
-                (map
-                 (match-lambda
-                   ((genecategory pmid email text createtime weburl)
-                    (blank-node
-                     (set gnt:geneCategory genecategory)
-                     (multiset dct:source
-                               (map (lambda (el) (if (string-null? el)
-                                                     ""
-                                                     (ontology 'pubmed: el)))
-                                    (string-split pmid #\space)))
-                     (set dct:creator (regexp-substitute/global #f "@.*$"
-                                                                email
-                                                                'pre
-                                                                ""
-                                                                'post))
-                     (set gnt:geneWikiEntry
-                          (annotate-field text '^^xsd:string))
-                     (set dct:created (annotate-field
-                                       createtime
-                                       '^^xsd:datetime))
-                     (set foaf:homepage weburl))))
-                 (map
-                  (cut string-split-substring <> "::::")
-                  comments))))))
-
-(define-transformer dump-ncbi-genewiki-entries
-  (tables (GeneRIF_BASIC)
-          "GROUP BY GeneId, comment, createtime")
-  (schema-triples
-   (gnt:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry))
-  (triples (ontology 'generif:
-                     (field GeneRIF_BASIC GeneId))
-    (set gnt:geneWikiEntryOfNCBI
-         (blank-node
-          (set gnt:geneWikiEntry
-               (annotate-field (field GeneRIF_BASIC comment)
-                               '^^xsd:string))
-          (multiset dct:source (map (lambda (el) (if (string-null? el)
-                                                     ""
-                                                     (ontology 'pubmed: el)))
-                                    (string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
-                                                  #\,)))
-          (set dct:created (annotate-field (time-unix->string
-                                            (field GeneRIF_BASIC createtime) "~5")
-                                           '^^xsd:datetime))))))
-
-
-
-(dump-with-documentation
- (name "GeneRIF Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("dct:" "<http://purl.org/dc/terms/>")
-    ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
-    ("ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>")
-    ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
-    ("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
-        ))
- (outputs
-   '(#:documentation "./docs/dump-generif.md"
-     #:rdf "./verified-data/dump-generif.ttl")))