From 4eff64e40ba0c25886db6966af7695a2710181ea Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 9 Feb 2026 09:40:51 +0300
Subject: Delete (temporarily) probeset tx.

This file is too big.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/probesets.scm | 123 -------------------------------------------------
 1 file changed, 123 deletions(-)
 delete mode 100755 examples/probesets.scm

(limited to 'examples')

diff --git a/examples/probesets.scm b/examples/probesets.scm
deleted file mode 100755
index 1bbfec8..0000000
--- a/examples/probesets.scm
+++ /dev/null
@@ -1,123 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-(use-modules (srfi srfi-1)
-             (srfi srfi-26)
-             (ice-9 getopt-long)
-             (ice-9 match)
-             (ice-9 regex)
-             (transform strings)
-             (transform sql)
-             (transform triples)
-             (transform special-forms))
-
-(define-transformer probeset->metadata
-  (tables (ProbeSet
-           (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))
-          "WHERE ProbeSet.Name IS NOT NULL AND TRIM(ProbeSet.Name) != ''")
-  (triples
-      (string->identifier "probeset" (field ProbeSet Name))
-    (set rdf:type 'gnc:probeset)
-    (set skos:prefLabel (field ProbeSet Name))
-    (set skos:altLabel (sanitize-rdf-string (field ProbeSet alias)))
-    (set gnt:uses_genechip (string->identifier "platform" (field GeneChip Name) #:separator "_"))
-    (set gnt:has_target_id
-         (field ("NULLIF(TRIM(ProbeSet.TargetId), '')"
-                 TargetId)))
-    (set gnt:symbol (field ProbeSet Symbol))
-    (set dct:description (sanitize-rdf-string (field ProbeSet description)))
-    (set gnt:targets_region
-         (sanitize-rdf-string
-          (field ("NULLIF(TRIM(ProbeSet.Probe_set_target_region), '')"
-                  Probe_set_target_region))))
-    (set gnt:chr (field ProbeSet Chr))
-    (set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
-    (set gnt:mb_mm8 (annotate-field (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))
-                                    '^^xsd:double))
-    (set gnt:has_specificity
-         (field ("IFNULL(ProbeSet.Probe_set_specificity, '')"
-                 Probe_set_specificity)))
-    (set gnt:has_blat_score
-         (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')"
-                 Probe_set_BLAT_score)))
-    (set gnt:has_blat_mb_start
-         (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')"
-                                 Probe_set_Blat_Mb_start))
-                         '^^xsd:double))
-    (set gnt:has_blat_mb_end
-         (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')"
-                                 Probe_set_Blat_Mb_end))
-                         '^^xsd:double))
-    (set gnt:has_blat_seq (sanitize-rdf-string (field ProbeSet BlatSeq)))
-    (set gnt:has_target_seq (sanitize-rdf-string (field ProbeSet TargetSeq)))
-    (set gnt:has_homologene_id (ontology 'homologene:
-                                         (field ("IFNULL(ProbeSet.HomoloGeneID, '')"
-                                                 HomoloGeneID))))
-    (set gnt:has_uniprot_id (ontology 'uniprot:
-                                      (field ("IFNULL(ProbeSet.UniProtID, '')"
-                                              UniProtID))))
-    (set gnt:has_pub_chem_id (ontology
-                              'pubchem:
-                              (field ("IFNULL(ProbeSet.PubChem_ID, '')"
-                                      PubChem_ID))))
-    (set gnt:has_kegg_id (ontology
-                          'kegg:
-                          (field ("IFNULL(ProbeSet.KEGG_ID, '')"
-                                  KEGG_ID))))
-    (set gnt:has_omim_id (ontology
-                          'omim:
-                          (let ((omim (field ("IFNULL(ProbeSet.OMIM, '')"
-                                              OMIM))))
-                            (if (number? omim)
-                                omim
-                                (regexp-substitute/global
-                                 #f "[^0-9]"
-                                 omim
-                                 'pre "" 'post)))))
-    (set gnt:has_chebi_id (ontology
-                         'chebi:
-                         (field ("IFNULL(ProbeSet.ChEBI_ID, '')"
-                                 ChEBI_ID))))))
-
-
-
-
-(let* ((option-spec
-        '((settings (single-char #\s) (value #t))
-          (output (single-char #\o) (value #t))
-          (documentation (single-char #\d) (value #t))))
-       (options (getopt-long (command-line) option-spec))
-       (settings (option-ref options 'settings #f))
-       (output (option-ref options 'output #f))
-       (documentation (option-ref options 'documentation #f))
-       (%connection-settings
-        (call-with-input-file settings
-          read)))
-  (with-documentation
-   (name "ProbeSet Metadata")
-   (connection %connection-settings)
-   (table-metadata? #f)
-   (prefixes
-    '(("gn:" "<http://genenetwork.org/id/>")
-      ("probeset:" "<http://genenetwork.org/probeset/>")
-      ("gnc:" "<http://genenetwork.org/category/>")
-      ("gnt:" "<http://genenetwork.org/term/>")
-      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-      ("kegg:" "<http://bio2rdf.org/ns/kegg#>")
-      ("pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
-      ("omim:" "<https://www.omim.org/entry/>")
-      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-      ("uniprot:" "<http://purl.uniprot.org/uniprot/>")
-      ("chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
-      ("dct:" "<http://purl.org/dc/terms/>")
-      ("owl:" "<http://www.w3.org/2002/07/owl#>")
-      ("homologene:" "<https://bio2rdf.org/homologene:>")
-      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-      ("qb:" "<http://purl.org/linked-data/cube#>")
-      ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
-      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
-   (inputs
-    (list probeset->metadata))
-   (outputs
-    `(#:documentation ,documentation
-      #:rdf ,output))))
-- 
cgit 1.4.1