From a002190cd1b9b3676e824837c7645169a1544e6f Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 30 Aug 2023 18:10:07 +0300
Subject: Delete this probeset-data tranform

* examples/probeset-data.scm: Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/probeset-data.scm | 98 ----------------------------------------------
 1 file changed, 98 deletions(-)
 delete mode 100755 examples/probeset-data.scm

(limited to 'examples')

diff --git a/examples/probeset-data.scm b/examples/probeset-data.scm
deleted file mode 100755
index ebb6a92..0000000
--- a/examples/probeset-data.scm
+++ /dev/null
@@ -1,98 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-(use-modules (srfi srfi-1)
-             (srfi srfi-26)
-             (ice-9 match)
-             (ice-9 regex)
-             (transform strings)
-             (transform sql)
-             (transform triples)
-             (transform special-forms))
-
-
-
-(define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
-
-
-(define-transformer probeset-data
-  (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
-   (gnc:probesetStatistics a skos:Concept)
-   (gnc:probesetStatistics
-    skos:description
-    "This is a set of controlled terms that are used to describe a given probeset's statistics")
-   (gnt:mean rdfs:domain gnc:probeset)
-   (gnt:locus rdfs:domain gnc:probeset)
-   (gnt:LRS rdfs:domain gnc:probeset)
-   (gnt:stdErr rdfs:domain gnc:probeset)
-   (gnt:stdErr rdfs:range xsd:double)
-   (gnt:pValue rdfs:domain gnc:probeset)
-   (gnt:pValue rdfs:range xsd:double)
-   (gnt:h2 rdfs:domain gnc:probeset)
-   (gnt:h2 rdfs:range xsd:double))
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global
-        #f "[^A-Za-z0-9:]"
-        (field
-         ("CONCAT(ProbeSetFreeze.Name, '_', IF(NULLIF(TRIM(ProbeSet.Name), ProbeSet.Id) IS NULL, '', TRIM(ProbeSet.Name)))"
-          probesetData))
-        'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:probesetStatistics)
-    (set gnt:hasProbeSet (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))"
-                                           ProbeSetIdName)))
-                               (probeset-id (field ProbeSet Id)))
-                           (string->identifier
-                            "probeset"
-                            (if (string-null? id)
-                                (number->string probeset-id)
-                                (regexp-substitute/global
-                                 #f "[^A-Za-z0-9:]"
-                                 id
-                                 'pre "_" 'post)))))
-    (set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
-                                  '^^xsd:double))
-    (set gnt:locus (field ProbeSetXRef Locus))
-    (set gnt:LRS (annotate-field
-                  (field ("IFNULL(ProbeSetXRef.LRS, '')" lrs))
-                  '^^xsd:double))
-    (set gnt:additive
-         (annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
-                         '^^xsd:double))
-    (set gnt:stdErr (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" stdErr))
-                                    '^^xsd:double))
-    (set gnt:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
-                                    '^^xsd:double))
-    (set gnt:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
-                                '^^xsd:double))))
-
-
-
-(with-documentation
- (name "Probeset Summary Statistics")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/id/>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("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 probeset-data))
- (outputs
-  '(#:documentation "./docs/probeset-summary-stats.md"
-    #:rdf "./verified-data/probeset-summary-stats.ttl")))
-- 
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