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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/probeset.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/probeset.scm')
-rwxr-xr-x | examples/probeset.scm | 71 |
1 files changed, 38 insertions, 33 deletions
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)))) |