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authorMunyoki Kilyungi2023-08-19 16:10:02 +0300
committerMunyoki Kilyungi2023-08-19 16:10:02 +0300
commitdcfe92323fa82c30a199e8d9640668800a93f47b (patch)
treeaa9a16d8273b2611d349a0aec353a95ad5a02b3e /examples
parentbc6e327b906f1c47be46ee397a3be46a222211f0 (diff)
downloadgn-transform-databases-dcfe92323fa82c30a199e8d9640668800a93f47b.tar.gz
Rename inbredSet identifier
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples')
-rwxr-xr-xexamples/dump-dataset-metadata.scm5
-rwxr-xr-xexamples/dump-genotype.scm5
-rwxr-xr-xexamples/dump-phenotype.scm7
-rwxr-xr-xexamples/dump-probesetfreeze.scm5
-rwxr-xr-xexamples/dump-species-metadata.scm2
5 files changed, 20 insertions, 4 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index e099bac..43ac144 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -159,7 +159,10 @@
(set gdmt:hasRightsInfo (string-downcase
(field DatasetStatus DatasetStatusName)))
(set gnt:belongsToInbredSet
- (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))
+ (string->identifier
+ "inbredSet" (field InbredSet Name)
+ #:separator ""
+ #:proc string-capitalize-first))
(set gnt:hasTissue (string->identifier "tissue"
(field Tissue Short_Name)))
(set gnt:usesNormalization
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 1024b90..661c57e 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -55,7 +55,10 @@
(field GenoFreeze CreateTime)
'^^xsd:date))
(set gnt:belongsToInbredSet
- (string->identifier "" (field InbredSet Name InbredSetName)))))
+ (string->identifier
+ "inbredSet" (field InbredSet Name)
+ #:separator ""
+ #:proc string-capitalize-first))))
(define-dump dump-genotypes
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index 8d04a80..203b2f3 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -79,6 +79,13 @@
(field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
Phenotype)))
(set rdf:type 'gnc:phenotype)
+ (set gnt:belongsToInbredSet
+ (string->identifier
+ "inbredSet" (field InbredSet Name)
+ #:separator ""
+ #:proc string-capitalize-first))
+ (set gnt:traitName
+ (field PublishXRef Id))
(set rdfs:label
(field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
Phenotype)))
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
index f528139..fab41b4 100755
--- a/examples/dump-probesetfreeze.scm
+++ b/examples/dump-probesetfreeze.scm
@@ -101,7 +101,10 @@
"tissue"
(field Tissue Short_Name)))
(set gnt:belongsToInbredSet
- (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
+ (string->identifier
+ "inbredSet" (field InbredSet Name)
+ #:separator ""
+ #:proc string-capitalize-first))))
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
index 6270fba..06daf33 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/dump-species-metadata.scm
@@ -161,7 +161,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
(gnt:mappingMethod a owl:ObjectProperty)
(gnt:mappingMethod rdfs:domain gnc:inbredSet))
(triples (string->identifier
- "" (field InbredSet Name)
+ "inbredSet" (field InbredSet Name)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:inbredSet)