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Diffstat (limited to 'examples/dump-probeset-metadata.scm')
-rwxr-xr-x | examples/dump-probeset-metadata.scm | 93 |
1 files changed, 0 insertions, 93 deletions
diff --git a/examples/dump-probeset-metadata.scm b/examples/dump-probeset-metadata.scm deleted file mode 100755 index 045a747..0000000 --- a/examples/dump-probeset-metadata.scm +++ /dev/null @@ -1,93 +0,0 @@ -#! /usr/bin/env guile -!# - -(use-modules (srfi srfi-1) - (srfi srfi-26) - (ice-9 match) - (ice-9 regex) - (dump strings) - (dump sql) - (dump triples) - (dump special-forms)) - - - -(define %connection-settings - (call-with-input-file (list-ref (command-line) 1) - read)) - - -(define-dump dump-probeset-metadata - (tables (ProbeSetXRef - (left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id") - (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")) - "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1") - (schema-triples - (gnt:hasProbeset rdfs:range rdfs:Literal)) - (triples - (string->identifier - "" - (regexp-substitute/global #f "[^A-Za-z0-9:]" - (field ProbeSetFreeze Name) - 'pre "_" 'post) - #:separator "" - #:proc string-capitalize-first) - (set rdf:type 'gnc:probesetData) - (set gnt:hasProbeset - (ontology - 'probeset: - (regexp-substitute/global - #f "[^A-Za-z0-9:]" - (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)" - name)) - 'pre "_" 'post))) - (set gnt:probesetOfDataset - (ontology - 'probeset: - (regexp-substitute/global #f "[^A-Za-z0-9:]" - (field ProbeSetFreeze Name) - 'pre "_" 'post))) - (set gnt:mean - (annotate-field - (field ("IFNULL(ProbeSetXRef.mean, '')" mean)) - '^^xsd:double)) - (set gnt:se - (annotate-field - (field ("IFNULL(ProbeSetXRef.se, '')" se)) - '^^xsd:double)) - (set gnt:locus (field ProbeSetXRef Locus)) - (set gn:LRS - (annotate-field - (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS)) - '^^xsd:double)) - (set gnt:pValue - (annotate-field - (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue)) - '^^xsd:double)) - (set gnt:additive - (annotate-field - (field ("IFNULL(ProbeSetXRef.additive, '')" additive)) - '^^xsd:double)) - (set gnt:h2 - (annotate-field - (field ("IFNULL(ProbeSetXRef.h2, '')" h2)) - '^^xsd:float)))) - - - -(dump-with-documentation - (name "Probeset Metadata") - (connection %connection-settings) - (table-metadata? #f) - (prefixes - '(("gn:" "<http://genenetwork.org/id/>") - ("gnc:" "<http://genenetwork.org/category/>") - ("gnt:" "<http://genenetwork.org/id/>") - ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") - ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") - ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) - (inputs - (list dump-probeset-metadata)) - (outputs - '(#:documentation "./docs/dump-probeset-metadata.md" - #:rdf "./verified-data/dump-probeset-metadata.ttl"))) |