diff options
Diffstat (limited to 'examples/phenotype.scm')
| -rwxr-xr-x | examples/phenotype.scm | 61 |
1 files changed, 34 insertions, 27 deletions
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) @@ -13,12 +14,6 @@ (transform special-forms)) - -(define %connection-settings - (call-with-input-file (list-ref (command-line) 1) - read)) - - (define-transformer phenotypes (tables (PublishXRef (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") @@ -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)))) + |