From 7121155871b500bf49e4f1ffa13ed66601acff8b Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 6 Jun 2023 14:41:50 +0300
Subject: Make geoSeries a link during dataset dump

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-dataset-metadata.scm | 10 +++++++---
 examples/dump-probesetfreeze.scm   |  1 +
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index 92e858c..5b57890 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -163,9 +163,12 @@
     (set gn:aboutTissue
          (sanitize-rdf-string (field Datasets AboutTissue)))
     (set gn:geoSeries
-         (and (not (string-prefix-ci? "no geo series"
-                                      (field Datasets GeoSeries)))
-              (field Datasets GeoSeries)))
+         (let ((s
+                (string-match "GSE[0-9]*"
+                              (field ("IFNULL(Datasets.GeoSeries, '')" GeoSeries)))))
+           (if s (ontology
+                  'geoSeries: (match:substring s))
+               "")))
     (set gn:title
          (regexp-substitute/global
           #f "^[Nn]one$"
@@ -226,6 +229,7 @@
        (prefix "dct:" "<http://purl.org/dc/terms/>")
        (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
        (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
        (prefix "gn:" "<http://genenetwork.org/>")
        (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
        (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
index 605e415..3e0c930 100755
--- a/examples/dump-probesetfreeze.scm
+++ b/examples/dump-probesetfreeze.scm
@@ -68,6 +68,7 @@
        (prefix "dct:" "<http://purl.org/dc/terms/>")
        (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
        (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
        (prefix "gn:" "<http://genenetwork.org/>")
        (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
        (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
-- 
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