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-phenotype.scm | 29 -----------------------------
 1 file changed, 29 deletions(-)

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

diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index f5a8c3c..6c52ebb 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -19,34 +19,6 @@
     read))
 
 
-
-;; These are phenotype datasets that don't have Infofile metadata
-(define-dump dump-publishfreeze
-  (tables (PublishFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
-           (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
-          "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoFileId IS NULL")
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                 (field PublishFreeze Name)
-                                 'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:phenotypeDataset)
-    (set rdfs:label (field PublishFreeze Name))
-    (set skos:prefLabel (field PublishFreeze FullName))
-    (set skos:altLabel (field PublishFreeze ShortName))
-    (set dct:created (annotate-field
-                      (field PublishFreeze CreateTime)
-                      '^^xsd:date))
-    (set gnt:belongsToSet
-         (string->identifier
-            "inbredSet" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first))))
-
 (define-dump dump-phenotypes
   (tables (PublishXRef
            (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
@@ -147,7 +119,6 @@
     ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
  (inputs
   (list
-   dump-publishfreeze
    dump-phenotypes))
  (outputs
   '(#:documentation "./docs/dump-phenotype.md"
-- 
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