Delete dump-published-phenotypes

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 0 insertions, 67 deletions

diff --git a/dump.scm b/dump.scm
index 2bd9cdf..5cfdd72 100755
--- a/dump.scm
+++ b/dump.scm
@@ -497,73 +497,6 @@ must be remedied."
     (set gn:datasetOfInbredSet
          (inbred-set-name->id (field InbredSet Name InbredSetName)))))
 
-;; Phenotype metadata
-(define-dump dump-published-phenotypes
-  (tables (PublishXRef
-           (inner-join
-            Phenotype
-            "ON PublishXRef.PhenotypeId = Phenotype.Id")
-           (inner-join
-            Publication
-            "ON PublishXRef.PublicationId =
-Publication.Id")
-           (inner-join PublishFreeze "USING (InbredSetId)"))
-          "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1")
-  (schema-triples
-   (gn:prePublicationDescription rdfs:range rdfs:Literal)
-   (gn:postPublicationDescription rdfs:range rdfs:Literal)
-   (gn:originalDescription rdfs:range rdfs:Literal)
-   (gn:units rdfs:range rdfs:Literal)
-   (gn:prePublicationAbbreviation rdfs:range rdfs:Literal)
-   (gn:postPublicationAbbreviation rdfs:range rdfs:Literal)
-   (gn:labCode rdfs:range rdfs:Literal)
-   (gn:submitter rdfs:range rdfs:Literal)
-   (gn:owner rdfs:range rdfs:Literal)
-   (gn:phenotypeOfDataset rdfs:range gn:dataset)
-   (gn:pubMedId rdfs:range rdfs:Literal)
-   (gn:publicationId rdfs:range gn:publication)
-   (gn:mean rdfs:range rdfs:Literal)
-   (gn:locus rdfs:range rdfs:Literal)
-   (gn:lrs rdfs:range rdfs:Literal)
-   (gn:additive rdfs:range rdfs:Literal)
-   (gn:sequence rdfs:range rdfs:Literal)
-   (gn:comments rdfs:range rdfs:Literal))
-  ;; In GN, a given trait is identified by the id of the PublishXRef!
-  (triples (string->identifier "phenotype"
-                               (number->string
-                                (field PublishXRef Id)))
-    (set rdf:type 'gn:phenotype)
-    (set rdf:type 'gn:phenotype)
-    (set gn:prePublicationDescription (field Phenotype Pre_publication_description))
-    (set gn:prePublicationDescription (field Phenotype Pre_publication_description))
-    (set gn:postPublicationDescription (field Phenotype Post_publication_description))
-    (set gn:originalDescription (field Phenotype Original_description))
-    (set gn:units (field Phenotype Units))
-    (set gn:prePublicationAbbreviation (field Phenotype Pre_publication_description))
-    (set gn:postPublicationAbbreviation (field Phenotype Post_publication_abbreviation))
-    (set gn:labCode (field Phenotype Lab_code))
-    (multiset gn:submitter
-              (map string-trim (string-split
-                                (field Phenotype Submitter) #\,)))
-    (multiset gn:owner
-              (map string-trim (string-split
-                                (field Phenotype Owner) #\,)))
-    (set gn:pubMedId (field Publication PubMed_ID))
-    (set gn:publicationId
-         (string->identifier
-          "publication"
-          (number->string (field Publication Id))))
-    (set gn:mean (field PublishXRef mean))
-    (set gn:locus (field PublishXRef Locus))
-    (set gn:lrs (field PublishXRef LRS))
-    (set gn:additive (field PublishXRef additive))
-    (set gn:sequence (field PublishXRef Sequence))
-    (set gn:comments (field PublishXRef comments))
-    (set gn:phenotypeOfDataset
-         (string->identifier "dataset"
-                             (field PublishFreeze Name)))))
-
-
 (define-dump dump-publication
   (tables (Publication))
   (schema-triples