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/dataset-metadata.scm | 75 +++++++++++++++++++++++--------------------
 examples/generif.scm          | 67 +++++++++++++++++++++-----------------
 examples/genotype.scm         | 56 +++++++++++++++++---------------
 examples/phenotype.scm        | 61 +++++++++++++++++++----------------
 examples/probeset.scm         | 71 +++++++++++++++++++++-------------------
 examples/publication.scm      | 58 ++++++++++++++++++---------------
 examples/species-metadata.scm | 63 ++++++++++++++++++------------------
 examples/tissue.scm           | 61 +++++++++++++++++++----------------
 8 files changed, 278 insertions(+), 234 deletions(-)

(limited to 'examples')

diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
index 783b2b7..8bb9607 100755
--- a/examples/dataset-metadata.scm
+++ b/examples/dataset-metadata.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))
-
-
-
 ;; One email ID in the Investigators table has spaces in it. This
 ;; function fixes that.
 (define (fix-email-id email)
@@ -356,32 +351,44 @@
 
 
 
-(with-documentation
- (name "Info files / Investigators Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("v:" "<http://www.w3.org/2006/vcard/ns#>")
-    ("foaf:" "<http://xmlns.com/foaf/0.1/>")
-    ("gdmt:" "<http://vocab.fairdatacollective.org/gdmt/>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("taxon:" "<http://purl.uniprot.org/taxonomy/>")
-    ("dct:" "<http://purl.org/dc/terms/>")))
- (inputs
-  (list info-files
-        publishfreeze
-        genofreeze
-        probesetfreeze
-        investigators
-        gene-chip))
- (outputs
-  '(#:documentation "./docs/info-pages.md"
-    #:rdf "/export/data/genenetwork-virtuoso/info-pages.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 "Info files / Investigators Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("v:" "<http://www.w3.org/2006/vcard/ns#>")
+      ("foaf:" "<http://xmlns.com/foaf/0.1/>")
+      ("gdmt:" "<http://vocab.fairdatacollective.org/gdmt/>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
+      ("gnt:" "<http://genenetwork.org/term/>")
+      ("gn:" "<http://genenetwork.org/id/>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("taxon:" "<http://purl.uniprot.org/taxonomy/>")
+      ("dct:" "<http://purl.org/dc/terms/>")))
+   (inputs
+    (list info-files
+          publishfreeze
+          genofreeze
+          probesetfreeze
+          investigators
+          gene-chip))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
+
 
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))))
diff --git a/examples/genotype.scm b/examples/genotype.scm
index 6fe60c9..830da0a 100755
--- a/examples/genotype.scm
+++ b/examples/genotype.scm
@@ -5,6 +5,7 @@
              (rnrs io ports)
              (srfi srfi-1)
              (srfi srfi-26)
+             (ice-9 getopt-long)
              (ice-9 match)
              (ice-9 regex)
              (transform strings)
@@ -14,12 +15,6 @@
 
 
 
-(define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
-
-
 (define (remap-species-identifiers str)
   "This procedure remaps identifiers to standard binominal. Obviously this should
    be sorted by correcting the database!"
@@ -103,22 +98,33 @@
 
 
 
-(with-documentation
- (name "Genotype Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("dct:" "<http://purl.org/dc/terms/>")
-    ("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
- (inputs
-  (list genotypes))
- (outputs
-  '(#:documentation "./docs/genotype.md"
-    #:rdf "/export/data/genenetwork-virtuoso/genotype.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 "Genotype Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("dct:" "<http://purl.org/dc/terms/>")
+      ("gn:" "<http://genenetwork.org/id/>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("gnt:" "<http://genenetwork.org/term/>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
+   (inputs
+    (list genotypes))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
diff --git a/examples/phenotype.scm b/examples/phenotype.scm
index 31d7972..772c2bc 100755
--- a/examples/phenotype.scm
+++ b/examples/phenotype.scm
@@ -5,6 +5,7 @@
              (rnrs io ports)
              (srfi srfi-1)
              (srfi srfi-26)
+             (ice-9 getopt-long)
              (ice-9 match)
              (ice-9 regex)
              (transform strings)
@@ -12,12 +13,6 @@
              (transform triples)
              (transform special-forms))
 
-
-
-(define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
 
 (define-transformer phenotypes
   (tables (PublishXRef
@@ -102,24 +97,36 @@
 
 
 
-(with-documentation
- (name "Phenotypes Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("dct:" "<http://purl.org/dc/terms/>")
-    ("gn:" "<http://genenetwork.org/id/>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/terms/>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("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#>")
-    ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
- (inputs
-  (list
-   phenotypes))
- (outputs
-  '(#:documentation "./docs/phenotype.md"
-    #:rdf "/export/data/genenetwork-virtuoso/phenotype.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 "Phenotypes Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("dct:" "<http://purl.org/dc/terms/>")
+      ("gn:" "<http://genenetwork.org/id/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("gnt:" "<http://genenetwork.org/terms/>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("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#>")
+      ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
+   (inputs
+    (list
+     phenotypes))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
+
diff --git a/examples/probeset.scm b/examples/probeset.scm
index 2dfdbc2..fa2fff6 100755
--- a/examples/probeset.scm
+++ b/examples/probeset.scm
@@ -3,19 +3,13 @@
 
 (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 probeset
   (tables (ProbeSet
@@ -156,29 +150,40 @@
 
 
 
-(with-documentation
- (name "ProbeSet Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("gn:" "<http://genenetwork.org/id/>")
-    ("probeset:" "<http://genenetwork.org/probeset/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("kegg:" "<http://bio2rdf.org/ns/kegg#>")
-    ("pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
-    ("omim:" "<https://www.omim.org/entry/>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("uniprot:" "<http://purl.uniprot.org/uniprot/>")
-    ("chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
-    ("dct:" "<http://purl.org/dc/terms/>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("homologene:" "<https://bio2rdf.org/homologene:>")
-    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
- (inputs
-  (list probeset))
- (outputs
-  '(#:documentation "./docs/probeset.md"
-    #:rdf "./verified-data/probeset.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 "ProbeSet Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("gn:" "<http://genenetwork.org/id/>")
+      ("probeset:" "<http://genenetwork.org/probeset/>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("gnt:" "<http://genenetwork.org/term/>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("kegg:" "<http://bio2rdf.org/ns/kegg#>")
+      ("pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+      ("omim:" "<https://www.omim.org/entry/>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("uniprot:" "<http://purl.uniprot.org/uniprot/>")
+      ("chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+      ("dct:" "<http://purl.org/dc/terms/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("homologene:" "<https://bio2rdf.org/homologene:>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
+   (inputs
+    (list probeset))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
diff --git a/examples/publication.scm b/examples/publication.scm
index d9e2aa5..81606b2 100755
--- a/examples/publication.scm
+++ b/examples/publication.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 publication
   (tables (Publication))
   (triples
@@ -59,23 +54,34 @@
 
 
 
-(with-documentation
- (name "Publications Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("gnt:" "<http://genenetwork.org/terms/>")
-    ("fabio:" "<http://purl.org/spar/fabio/>")
-    ("dct:" "<http://purl.org/dc/terms/>")
-    ("prism:" "<http://prismstandard.org/namespaces/basic/2.0/>")
-    ("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")))
- (inputs
-  (list publication))
- (outputs
-  '(#:documentation "./docs/publication.md"
-    #:rdf "./verified-data/publication.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 "Publications Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("gnt:" "<http://genenetwork.org/terms/>")
+      ("fabio:" "<http://purl.org/spar/fabio/>")
+      ("dct:" "<http://purl.org/dc/terms/>")
+      ("prism:" "<http://prismstandard.org/namespaces/basic/2.0/>")
+      ("gn:" "<http://genenetwork.org/id/>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")))
+   (inputs
+    (list publication))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
diff --git a/examples/species-metadata.scm b/examples/species-metadata.scm
index b67c0bc..b330b12 100755
--- a/examples/species-metadata.scm
+++ b/examples/species-metadata.scm
@@ -3,21 +3,14 @@
 
 (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 (remap-species-identifiers str)
   "This procedure remaps identifiers to standard binominal. Obviously this should
    be sorted by correcting the database!"
@@ -201,26 +194,34 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
 
 
 
-(with-documentation
- (name "Species Metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
- (inputs
-  (list
-   inbred-set
-   species
-   strain
-   mapping-method
-   avg-method))
- (outputs
-  '(#:documentation "./docs/species-metadata.md"
-    #:rdf "/export/data/genenetwork-virtuoso/species-metadata.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 "Species Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("gn:" "<http://genenetwork.org/id/>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("gnt:" "<http://genenetwork.org/term/>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
+   (inputs
+    (list inbred-set species strain mapping-method avg-method))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
+
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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