From 0036a4f63fa3bef6eea95fe635eb23d4dc070727 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 19 Jul 2023 20:14:02 +0300
Subject: Dump probeset-metadata using the new syntax

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-probeset-metadata.scm | 65 ++++++++++++++-----------------------
 1 file changed, 24 insertions(+), 41 deletions(-)

(limited to 'examples/dump-probeset-metadata.scm')

diff --git a/examples/dump-probeset-metadata.scm b/examples/dump-probeset-metadata.scm
index b0c4853..6da1eb0 100755
--- a/examples/dump-probeset-metadata.scm
+++ b/examples/dump-probeset-metadata.scm
@@ -16,9 +16,6 @@
   (call-with-input-file (list-ref (command-line) 1)
     read))
 
-(define %dump-directory
-  (list-ref (command-line) 2))
-
 
 (define-dump dump-probeset-metadata
   (tables (ProbeSetXRef
@@ -27,14 +24,14 @@
           "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1")
   (schema-triples
    (gn:probesetData rdfs:range gn:probeset)
-   (gn:hasProbeset rdfs:range rdfs:Literal))
+   (gn-term:hasProbeset rdfs:range rdfs:Literal))
   (triples
       (string->identifier
        "probesetData"
        (field ("CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id))"
                ProbeSetName)))
     (set rdf:type 'gn:probesetData)
-    (set gn:hasProbeset
+    (set gn-term:hasProbeset
          (ontology
           'probeset:
           (regexp-substitute/global
@@ -42,66 +39,52 @@
            (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
                    name))
            'pre "_" 'post)))
-    (set gn:probesetOfDataset
+    (set gn-term:probesetOfDataset
          (ontology
           'probeset:
           (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                     (field ProbeSetFreeze Name)
                                     'pre "_" 'post)))
-    (set gn:mean
+    (set gn-term:mean
          (annotate-field
           (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
           '^^xsd:double))
-    (set gn:se
+    (set gn-term:se
          (annotate-field
           (field ("IFNULL(ProbeSetXRef.se, '')" se))
           '^^xsd:double))
-    (set gn:locus (field ProbeSetXRef Locus))
+    (set gn-term:locus (field ProbeSetXRef Locus))
     (set gn:LRS
          (annotate-field
           (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
           '^^xsd:double))
-    (set gn:pValue
+    (set gn-term:pValue
          (annotate-field
           (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
           '^^xsd:double))
-    (set gn:additive
+    (set gn-term:additive
          (annotate-field
           (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
           '^^xsd:double))
-    (set gn:h2
+    (set gn-term:h2
          (annotate-field
           (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
           '^^xsd:float))))
 
 
 
-(call-with-target-database
- %connection-settings
- (lambda (db)
-   (with-output-to-file (string-append %dump-directory "dump-probeset-metadata.ttl")
-     (lambda ()
-       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
-       (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 "gn:" "<http://genenetwork.org/>")
-       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
-       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
-       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
-       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
-       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
-       (prefix "omim:" "<https://www.omim.org/entry/>")
-       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
-       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
-       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
-       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
-       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
-       (prefix "up:" "<http://purl.uniprot.org/core/>")
-       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-       (prefix "probeset:" "<http://genenetwork.org/probeset/>")
-       (newline)
-       (dump-probeset-metadata db))
-     #:encoding "utf8")))
+(dump-with-documentation
+ (name "Probeset Metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+  '(("gn:" "<http://genenetwork.org/id/>")
+    ("gn-term:" "<http://genenetwork.org/id/>")
+    ("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 dump-probeset-metadata))
+ (outputs
+  '(#:documentation "./docs/dump-probeset-metadata.md"
+    #:rdf "./verified-data/dump-probeset-metadata.ttl")))
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