diff options
Diffstat (limited to 'examples/dump-probeset-data.scm')
| -rwxr-xr-x | examples/dump-probeset-data.scm | 53 |
1 files changed, 32 insertions, 21 deletions
diff --git a/examples/dump-probeset-data.scm b/examples/dump-probeset-data.scm index c4e55ab..7ab723d 100755 --- a/examples/dump-probeset-data.scm +++ b/examples/dump-probeset-data.scm @@ -20,10 +20,14 @@ (define-dump dump-probeset-data (tables (ProbeSetXRef - (left-join ProbeSet "ON ProbeSet.Id = ProbeSetXRef.ProbeSetId") - (left-join ProbeSetFreeze "ON ProbeSet.ProbeSetFreezeId = ProbeSetFreeze.Id"))) - "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1" + (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 + (gnc:probesetStatistics a skos:Concept) + (gnc:probesetStatistics + skos:description + "This is a set of controlled terms that are used to describe a given probeset's statistics") (gnt:mean rdfs:domain gnc:probeset) (gnt:locus rdfs:domain gnc:probeset) (gnt:LRS rdfs:domain gnc:probeset) @@ -33,25 +37,32 @@ (gnt:pValue rdfs:range xsd:double) (gnt:h2 rdfs:domain gnc:probeset) (gnt:h2 rdfs:range xsd:double)) - (triples (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))" - ProbeSetIdName))) - (probeset-id (field ProbeSet Id))) - (if (string-null? id) - (string->identifier - "probeset" - (number->string - probeset-id)) - (string->identifier - "" - (regexp-substitute/global - #f "[^A-Za-z0-9:]" - id - 'pre "_" 'post) - #:separator "" - #:proc string-capitalize-first))) + (triples + (string->identifier + "" + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field + ("CONCAT(ProbeSetFreeze.Name, '_', IF(NULLIF(TRIM(ProbeSet.Name), ProbeSet.Id) IS NULL, '', TRIM(ProbeSet.Name)))" + probesetData)) + 'pre "_" 'post) + #:separator "" + #:proc string-capitalize-first) + (set rdf:type 'gnc:probesetStatistics) + (set gnt:hasProbeSet (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))" + ProbeSetIdName))) + (probeset-id (field ProbeSet Id))) + (string->identifier + "probeset" + (if (string-null? id) + (number->string probeset-id) + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + id + 'pre "_" 'post))))) (set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean)) '^^xsd:double)) - (set gnt:locus (field PublishXRef Locus)) + (set gnt:locus (field ProbeSetXRef Locus)) (set gnt:LRS (annotate-field (field ("IFNULL(ProbeSetXRef.LRS, '')" lrs)) '^^xsd:double)) @@ -87,7 +98,7 @@ ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) (inputs - (list dump-probeset-metadata)) + (list dump-probeset-data)) (outputs '(#:documentation "./docs/dump-probeset-summary-stats.md" #:rdf "./verified-data/dump-probeset-summary-stats.ttl"))) |