Rename dump-probeset-metadata -> dump-probeset-data

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

1 files changed, 0 insertions, 93 deletions

diff --git a/examples/dump-probeset-metadata.scm b/examples/dump-probeset-metadata.scm
deleted file mode 100755
index 045a747..0000000
--- a/examples/dump-probeset-metadata.scm
+++ /dev/null
@@ -1,93 +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-dump dump-probeset-metadata
-  (tables (ProbeSetXRef
-           (left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
-           (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"))
-          "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1")
-  (schema-triples
-   (gnt:hasProbeset rdfs:range rdfs:Literal))
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                 (field ProbeSetFreeze Name)
-                                 'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:probesetData)
-    (set gnt:hasProbeset
-         (ontology
-          'probeset:
-          (regexp-substitute/global
-           #f "[^A-Za-z0-9:]"
-           (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
-                   name))
-           'pre "_" 'post)))
-    (set gnt:probesetOfDataset
-         (ontology
-          'probeset:
-          (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                    (field ProbeSetFreeze Name)
-                                    'pre "_" 'post)))
-    (set gnt:mean
-         (annotate-field
-          (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
-          '^^xsd:double))
-    (set gnt:se
-         (annotate-field
-          (field ("IFNULL(ProbeSetXRef.se, '')" se))
-          '^^xsd:double))
-    (set gnt:locus (field ProbeSetXRef Locus))
-    (set gn:LRS
-         (annotate-field
-          (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
-          '^^xsd:double))
-    (set gnt:pValue
-         (annotate-field
-          (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
-          '^^xsd:double))
-    (set gnt:additive
-         (annotate-field
-          (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
-          '^^xsd:double))
-    (set gnt:h2
-         (annotate-field
-          (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
-          '^^xsd:float))))
-
-
-
-(dump-with-documentation
- (name "Probeset Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/id/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
- (inputs
-  (list dump-probeset-metadata))
- (outputs
-  '(#:documentation "./docs/dump-probeset-metadata.md"
-    #:rdf "./verified-data/dump-probeset-metadata.ttl")))