From 99cef5dab86b93fb6f7d600297bd4fbb54622a64 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 21 Aug 2023 15:37:37 +0300
Subject: Remove hard-coded paths

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/tissue.scm | 61 +++++++++++++++++++++++++++++------------------------
 1 file changed, 33 insertions(+), 28 deletions(-)

(limited to 'examples/tissue.scm')

diff --git a/examples/tissue.scm b/examples/tissue.scm
index 22b715e..ce9f345 100755
--- a/examples/tissue.scm
+++ b/examples/tissue.scm
@@ -3,48 +3,53 @@
 
 (use-modules (srfi srfi-1)
              (srfi srfi-26)
+             (ice-9 getopt-long)
              (ice-9 match)
              (ice-9 regex)
              (transform strings)
              (transform sql)
              (transform triples)
              (transform special-forms))
-
-
-
-(define %connection-settings
-    (call-with-input-file (list-ref (command-line) 1)
-			  read))
-
 
 
 (define-transformer 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
    (gnc:tissue a skos:Concept))
   ;; 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 'gnc:tissue)
-	   (set rdfs:label (field Tissue Name))))
+    (set rdf:type 'gnc:tissue)
+    (set rdfs:label (field Tissue Name))))
 
 
 
-(with-documentation
- (name "Tissue Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("gn:" "<http://genenetwork.org/id/>")
-    ("gnt:" "<http://genenetwork.org/terms/>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
- (inputs
-  (list tissue))
- (outputs
-  '(#:documentation "./docs/tissue.md"
-    #:rdf "./verified-data/tissue.ttl")))
+(let* ((option-spec
+        '((settings (single-char #\s) (value #t))
+          (output (single-char #\o) (value #t))
+          (documentation (single-char #\d) (value #t))))
+       (options (getopt-long (command-line) option-spec))
+       (settings (option-ref options 'settings #f))
+       (output (option-ref options 'output #f))
+       (documentation (option-ref options 'documentation #f))
+       (%connection-settings
+        (call-with-input-file settings
+          read)))
+  (with-documentation
+   (name "Tissue Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("gn:" "<http://genenetwork.org/id/>")
+      ("gnt:" "<http://genenetwork.org/terms/>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
+   (inputs
+    (list tissue))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
-- 
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