Remove "dump-" prefix

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

1 files changed, 0 insertions, 124 deletions

diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
deleted file mode 100755
index a055039..0000000
--- a/examples/dump-genotype.scm
+++ /dev/null
@@ -1,124 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-(use-modules (rnrs programs)
-             (rnrs io ports)
-             (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 (remap-species-identifiers str)
-  "This procedure remaps identifiers to standard binominal. Obviously this should
-   be sorted by correcting the database!"
-  (match str
-    ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
-    ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
-    ["Macaca mulatta" "Macaca nemestrina"]
-    ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
-    [str str]))
-
-(define-transformer dump-genotypes
-  (tables (Geno
-           (left-join Species "USING (SpeciesId)")))
-  (schema-triples
-   (gnc:genotype a skos:Concept)
-   (gnc:genotype
-    skos:description
-    "This is a set of controlled terms that are used to describe a given genotype")
-   (gnt:chr a owl:ObjectProperty)
-   (gnt:chr skos:description "This resource is located on a given chromosome")
-   (gnt:chr rdfs:domain gnc:genotype)
-   (gnt:mb a owl:ObjectProperty)
-   (gnt:mb skos:definition "The size of this resource in Mb")
-   (gnt:mb rdfs:domain gnc:genotype)
-   (gnt:mbMm8 a owl:ObjectProperty)
-   (gnt:mbMm8 skos:definition "TODO")
-   (gnt:mbMm8 rdfs:domain gnc:genotype)
-   (gnt:mb2016 a owl:ObjectProperty)
-   (gnt:mb2016 skos:definition "TODO")
-   (gnt:mb2016 rdfs:domain gnc:genotype)
-   (gnt:hasSequence a owl:ObjectProperty)
-   (gnt:hasSequence skos:definition "This resource has a given sequence")
-   (gnt:hasSequence rdfs:domain gnc:genotype)
-   (gnt:hasSource a owl:ObjectProperty)
-   (gnt:hasSource rdfs:domain gnc:genotype)
-   (gnt:hasSource skos:definition "This resource was obtained from this given source")
-   (gnt:hasAltSourceName a owl:ObjectProperty)
-   (gnt:hasAltSourceName rdfs:domain gnc:genotype)
-   (gnt:hasAltSourceName
-    skos:definition
-    "The alternative name this resource was obtained from")
-   (gnt:chrNum a owl:ObjectProperty)
-   (gnt:chrNum rdfs:domain gnc:genotype)
-   (gnt:chrNum skos:definition "The chromosome number for this resource")
-   (gnt:chrNum skos:definition "The chromosome number for this resource"))
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global
-        #f "[^A-Za-z0-9:]"
-        (field Geno Name)
-        'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:genotype)
-    (set skos:prefLabel (sanitize-rdf-string (field Geno Name)))
-    (set gnt:chr (field Geno Chr))
-    (set gnt:mb (annotate-field
-                 (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
-    (set gnt:mbMm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8))
-                                   '^^xsd:double))
-    (set gnt:mb2016
-         (annotate-field (field ("IFNULL(Geno.Mb_2016, '')" Mb_2016))
-                         '^^xsd:double))
-    (set gnt:hasSequence (field Geno Sequence))
-    (set gnt:hasSource (field Geno Source))
-    ;; Only dump Source2 if it differs from Source
-    (set gnt:hasAltSourceName
-         (field ("IF((Source2 = Source), NULL, Source2)"
-                 Source2)))
-    (set gnt:belongsToSpecies
-         (string->identifier
-          "" (remap-species-identifiers (field Species Fullname))
-          #:separator ""
-          #:proc string-capitalize-first))
-    (set gnt:chrNum
-         (annotate-field
-          (field Geno chr_num)
-          '^^xsd:int))
-    (set rdfs:comments (field Geno Comments))))
-
-
-
-(dump-with-documentation
- (name "Genotype Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("dct:" "<http://purl.org/dc/terms/>")
-    ("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
- (inputs
-  (list dump-genotypes))
- (outputs
-  '(#:documentation "./docs/dump-genotype.md"
-    #:rdf "/export/data/genenetwork-virtuoso/dump-genotype.ttl")))