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author | Munyoki Kilyungi | 2023-08-21 15:37:37 +0300 |
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committer | Munyoki Kilyungi | 2023-08-21 17:52:07 +0300 |
commit | 99cef5dab86b93fb6f7d600297bd4fbb54622a64 (patch) | |
tree | e3d607fbb53e4ffdc0f94163a26010ab3aa3203f /examples/generif.scm | |
parent | 8e1e4cceab516afab46ccced63ca9edab663ca11 (diff) | |
download | gn-transform-databases-99cef5dab86b93fb6f7d600297bd4fbb54622a64.tar.gz |
Remove hard-coded paths
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/generif.scm')
-rwxr-xr-x | examples/generif.scm | 67 |
1 files changed, 37 insertions, 30 deletions
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)))) |