From 3494fa35f332e0da6e4d2c76eac0a286fa4f5646 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 17 Jul 2023 23:03:07 +0300
Subject: Dump tissue metadata with documentation

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-tissue.scm | 57 ++++++++++++++++--------------------------------
 1 file changed, 19 insertions(+), 38 deletions(-)

diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm
index b1104ab..4998cff 100755
--- a/examples/dump-tissue.scm
+++ b/examples/dump-tissue.scm
@@ -13,53 +13,34 @@
 
 
 (define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
-(define %dump-directory
-  (list-ref (command-line) 2))
+    (call-with-input-file (list-ref (command-line) 1)
+			  read))
 
 
 
 (define-dump dump-tissue
-  ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
-  ;; and BIRN_lex_Name are mostly NULL.
-  (tables (Tissue))
+    ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
+    ;; and BIRN_lex_Name are mostly NULL.
+    (tables (Tissue))
   (schema-triples
    (gn:name rdfs:range rdfs:Literal))
   ;; Hopefully the Short_Name field is distinct and can be used as an
   ;; identifier.
   (triples (string->identifier "tissue" (field Tissue Short_Name))
-    (set rdf:type 'gn:tissue)
-    (set gn:name (field Tissue Name))))
+	   (set rdf:type 'gn:tissue)
+	   (set gn:name (field Tissue Name))))
 
 
 
-(call-with-target-database
- %connection-settings
- (lambda (db)
-   (with-output-to-file (string-append %dump-directory "dump-tissue.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#>")
-       (newline)
-       (dump-tissue db))
-     #:encoding "utf8")))
+(dump-with-documentation
+ (name "Tissue Metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+  (("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+   ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+   ("gn:" "<http://genenetwork.org/terms/>")))
+ (inputs
+  (dump-tissue))
+ (outputs
+  (#:documentation "./docs/dump-tissue.md" #:rdf "./verified-data/dump-tissue.ttl")))
-- 
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