From a1c634f5208b93edbde3d27a83ff60bc5dab8ca8 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 15 Aug 2023 20:21:30 +0300 Subject: Rename dump-probeset-metadata -> dump-probeset-data Signed-off-by: Munyoki Kilyungi --- examples/dump-probeset-data.scm | 53 ++++++++++++--------- examples/dump-probeset-metadata.scm | 93 ------------------------------------- 2 files changed, 32 insertions(+), 114 deletions(-) delete mode 100755 examples/dump-probeset-metadata.scm (limited to 'examples') 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:" "") ("xsd:" ""))) (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"))) 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:" "") - ("gnc:" "") - ("gnt:" "") - ("rdf:" "") - ("rdfs:" "") - ("xsd:" ""))) - (inputs - (list dump-probeset-metadata)) - (outputs - '(#:documentation "./docs/dump-probeset-metadata.md" - #:rdf "./verified-data/dump-probeset-metadata.ttl"))) -- cgit v1.2.3