diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/dump-dataset-metadata.scm | 50 |
1 files changed, 21 insertions, 29 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm index 789e298..53c381c 100755 --- a/examples/dump-dataset-metadata.scm +++ b/examples/dump-dataset-metadata.scm @@ -16,9 +16,6 @@ (call-with-input-file (list-ref (command-line) 1) read)) -(define %dump-directory - (list-ref (command-line) 2)) - ;; One email ID in the Investigators table has spaces in it. This @@ -150,8 +147,7 @@ (field Investigators Email))) (set gn:datasetOfOrganization (field ("CAST(CONVERT(BINARY CONVERT(Organizations.OrganizationName USING latin1) USING utf8) AS VARCHAR(1500))" Organizations))) - (set gn:accessionId (string-append "GN" (number->string - (field InfoFiles GN_AccesionId)))) + (set gn:accessionId (format #f "GN~a" (field InfoFiles GN_AccesionId))) (set gn:datasetStatusName (string-downcase (field DatasetStatus DatasetStatusName))) (set gn:datasetOfInbredSet @@ -234,27 +230,23 @@ -(call-with-target-database - %connection-settings - (lambda (db) - (with-output-to-file (string-append %dump-directory "dump-info-pages.ttl") - (lambda () - (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 "geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>") - (prefix "gn:" "<http://genenetwork.org/>") - (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") - (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") - (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 "probeset:" "<http://genenetwork.org/probeset/>") - (prefix "dataset:" "<http://genenetwork.org/dataset/>") - (newline) - (dump-info-files db) - (dump-investigators db)) - #:encoding "utf8"))) +(dump-with-documentation + (name "Info files / Investigators Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + (("dct:" "<http://purl.org/dc/terms/>") + ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>") + ("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/>") + ("foaf:" "<http://xmlns.com/foaf/0.1/>") + ("taxon:" "<http://purl.uniprot.org/taxonomy/>") + ("dataset:" "<http://genenetwork.org/dataset/>"))) + (inputs + (dump-info-files + dump-investigators)) + (outputs + (#:documentation "./docs/dump-info-pages.md" + #:rdf "./verified-data/dump-info-pages.ttl"))) + |