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| -rwxr-xr-x | examples/phenotype-datasets.scm | 74 |
1 files changed, 74 insertions, 0 deletions
diff --git a/examples/phenotype-datasets.scm b/examples/phenotype-datasets.scm new file mode 100755 index 0000000..9354926 --- /dev/null +++ b/examples/phenotype-datasets.scm @@ -0,0 +1,74 @@ +#! /usr/bin/env guile +!# + +(use-modules (rnrs programs) + (rnrs io ports) + (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-transformer gn:set->gn:dataset + (tables (Datasets + (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") + (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") + (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")) + "WHERE PublishFreeze.public > 0 GROUP BY Datasets.DatasetId") + (schema-triples + (gnt:has_phenotype_data rdf:type owl:ObjectProperty) + (gnt:has_phenotype_data rdfs:label "this resources has this phenotype data.") + (gnt:has_phenotype_data rdfs:comment "Associates a resource with its phenotype data.") + (gnt:has_phenotype_data rdfs:domain gnc:set) + (gnt:has_phenotype_data rdfs:range dcat:Dataset) + (gnt:has_phenotype_data rdfs:subPropertyOf dct:relation)) + (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") + (set gnt:has_phenotype_data (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")))) + +(define-transformer gn:dataset->gn:set + (tables (Datasets + (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") + (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") + (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")) + "WHERE PublishFreeze.public > 0 GROUP BY Datasets.DatasetId") + (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_") + (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + + +(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 "Genotype Datasets") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("dcat:" "<http://www.w3.org/ns/dcat#>") + ("dct:" "<http://purl.org/dc/terms/>") + ("gn:" "<http://rdf.genenetwork.org/v1/id/>") + ("gnc:" "<http://rdf.genenetwork.org/v1/category/>") + ("gnt:" "<http://rdf.genenetwork.org/v1/term/>") + ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + ("owl:" "<http://www.w3.org/2002/07/owl#>") + ("skos:" "<http://www.w3.org/2004/02/skos/core#>") + ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>") + ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) + (inputs + (list gn:set->gn:dataset gn:dataset->gn:set)) + (outputs + `(#:documentation ,documentation + #:rdf ,output)))) |