From add95e737f61fdf3e8f244dd7ebedca963514bb7 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 21 Aug 2023 14:41:23 +0300
Subject: Move dumps related to datasets to one place

* examples/dump-dataset-metadata.scm: Add dump-gene-chip,
dump-publishfreeze, dump-genofreeze, dump-probesetfreeze
* examples/dump-genotype.scm: Delete dump-genofreeze.
* examples/dump-phenotype.scm: Delete dump-publishfreeze.
* examples/dump-probesetfreeze.scm: Delete file
---
 examples/dump-genotype.scm | 34 +---------------------------------
 1 file changed, 1 insertion(+), 33 deletions(-)

(limited to 'examples/dump-genotype.scm')

diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 04f1af0..30e7796 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -30,37 +30,6 @@
     ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
     [str str]))
 
-(define-dump dump-genofreeze
-  (tables (GenoFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
-           (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
-          "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global
-        #f "[^A-Za-z0-9:]"
-        (regexp-substitute/global
-         #f "[^A-Za-z0-9:]"
-         (field GenoFreeze Name)
-         'pre "_" 'post)
-        'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:genotypeDataset)
-    (set rdfs:label (field GenoFreeze Name))
-    (set skos:prefLabel (field GenoFreeze FullName))
-    (set skos:altLabel (field GenoFreeze ShortName))
-    (set dct:created (annotate-field
-                      (field GenoFreeze CreateTime)
-                      '^^xsd:date))
-    (set gnt:belongsToSet
-         (string->identifier
-            "inbredSet" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first))))
-
-
 (define-dump dump-genotypes
   (tables (Geno
            (left-join Species "USING (SpeciesId)")))
@@ -149,8 +118,7 @@
     ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
  (inputs
-  (list dump-genofreeze
-        dump-genotypes))
+  (list dump-genotypes))
  (outputs
   '(#:documentation "./docs/dump-genotype.md"
     #:rdf "/export/data/genenetwork-virtuoso/dump-genotype.ttl")))
-- 
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