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/generif.scm | 67 +++++++++++++++++++++++++++++-----------------------
 1 file changed, 37 insertions(+), 30 deletions(-)

(limited to 'examples/generif.scm')

diff --git a/examples/generif.scm b/examples/generif.scm
index 76f55ee..170cf0c 100755
--- a/examples/generif.scm
+++ b/examples/generif.scm
@@ -3,6 +3,7 @@
 
 (use-modules (srfi srfi-1)
              (srfi srfi-26)
+             (ice-9 getopt-long)
              (ice-9 match)
              (ice-9 regex)
              (transform strings)
@@ -12,12 +13,6 @@
 
 
 
-(define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
-
-
 (define-transformer genewiki-symbols
   (tables (GeneRIF_BASIC
            (left-join Species "USING (SpeciesId)"))
@@ -124,27 +119,39 @@
 
 
 
-(with-documentation
- (name "GeneRIF 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/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("dct:" "<http://purl.org/dc/terms/>")
-    ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
-    ("ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>")
-    ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
-    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")))
- (inputs
-  (list ;; genewiki-symbols
-        gn-genewiki-entries
-        ;; ncbi-genewiki-entries
-        ))
- (outputs
-   '(#:documentation "./docs/generif.md"
-     #:rdf "./verified-data/generif.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 "GeneRIF 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/id/>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("gnt:" "<http://genenetwork.org/term/>")
+      ("dct:" "<http://purl.org/dc/terms/>")
+      ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+      ("ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>")
+      ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")))
+   (inputs
+    (list ;; genewiki-symbols
+     gn-genewiki-entries
+     ;; ncbi-genewiki-entries
+     ))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
-- 
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