diff options
Diffstat (limited to 'examples/publication.scm')
| -rwxr-xr-x | examples/publication.scm | 58 |
1 files changed, 32 insertions, 26 deletions
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)))) |