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authorMunyoki Kilyungi2023-07-17 23:03:21 +0300
committerMunyoki Kilyungi2023-07-21 14:36:39 +0300
commitc607d087183919f9dc8cc27edac4232650dfb67b (patch)
tree5608b82bf7228d53734dcfe6f74410ef81fc1a37
parent252aa900fcdc28546cd21741b982a00a55acf606 (diff)
downloadgn-transform-databases-c607d087183919f9dc8cc27edac4232650dfb67b.tar.gz
Dump publication metadata with documentation
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
-rwxr-xr-xexamples/dump-publication.scm51
1 files changed, 17 insertions, 34 deletions
diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm
index 784d815..ff46d3d 100755
--- a/examples/dump-publication.scm
+++ b/examples/dump-publication.scm
@@ -13,11 +13,8 @@
(define %connection-settings
- (call-with-input-file (list-ref (command-line) 1)
- read))
-
-(define %dump-directory
- (list-ref (command-line) 2))
+ (call-with-input-file (list-ref (command-line) 1)
+ read))
@@ -65,32 +62,18 @@
-(call-with-target-database
- %connection-settings
- (lambda (db)
- (with-output-to-file (string-append %dump-directory "dump-publication.ttl")
- (lambda ()
- (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
- (prefix "dct:" "<http://purl.org/dc/terms/>")
- (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
- (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
- (prefix "gn:" "<http://genenetwork.org/>")
- (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
- (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
- (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
- (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
- (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
- (prefix "omim:" "<https://www.omim.org/entry/>")
- (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
- (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
- (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
- (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
- (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
- (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
- (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
- (prefix "up:" "<http://purl.uniprot.org/core/>")
- (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
- (prefix "publication:" "<http://genenetwork.org/publication/>")
- (newline)
- (dump-publication db))
- #:encoding "utf8")))
+(dump-with-documentation
+ (name "Publications 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/terms/>")
+ ("publication:" "<http://genenetwork.org/publication/>")
+ ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
+ (inputs
+ (dump-publication))
+ (outputs
+ (#:documentation "./docs/dump-publication.md"
+ #:rdf "./verified-data/dump-publication.md")))