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author | Munyoki Kilyungi | 2023-08-21 14:54:21 +0300 |
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committer | Munyoki Kilyungi | 2023-08-21 14:56:57 +0300 |
commit | 51b3c0548c98e0bc05e11a89cbf6b75d31b9f8d5 (patch) | |
tree | ab3d7c6f589ed8480f0a9d451566681bcfd8eaaf /examples/dump-phenotype.scm | |
parent | 849874fdfe11003f05abe5f82efde974a8c8a388 (diff) | |
download | gn-transform-databases-51b3c0548c98e0bc05e11a89cbf6b75d31b9f8d5.tar.gz |
Remove "dump-" prefix
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/dump-phenotype.scm')
-rwxr-xr-x | examples/dump-phenotype.scm | 125 |
1 files changed, 0 insertions, 125 deletions
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm deleted file mode 100755 index b7ae003..0000000 --- a/examples/dump-phenotype.scm +++ /dev/null @@ -1,125 +0,0 @@ -#! /usr/bin/env guile -!# - -(use-modules (rnrs programs) - (rnrs io ports) - (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-transformer dump-phenotypes - (tables (PublishXRef - (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") - (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") - (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) - "WHERE PublishXRef.InbredSetId IN (SELECT PublishFreeze.InbredSetId FROM PublishFreeze)") - (schema-triples - (gnc:phenotype a skos:Concept) - (gnc:phenotype skos:description "This is a set of controlled terms that are used to describe a given phenotype") - (gnt:abbreviation a owl:ObjectProperty) - (gnt:abbreviation rdfs:domain gnc:phenotype) - (gnt:abbreviation skos:definition "The abbreviation used for this resource") - (gnt:traitName a owl:ObjectProperty) - (gnt:traitName rdfs:domain gnc:phenotype) - (gnt:traitName skos:definition "The trait Name of this resource") - (gnt:labCode a owl:ObjectProperty) - (gnt:labCode rdfs:domain gnc:phenotype) - (gnt:submitter a owl:ObjectProperty) - (gnt:submitter rdfs:domain gnc:phenotype) - (gnt:submitter skos:definition "A person who submitted this resource to GN") - (gnt:mean rdfs:domain gnc:phenotype) - (gnt:mean rdfs:range xsd:double) - (gnt:LRS rdfs:domain gnc:phenotype) - (gnt:LRS rdfs:range xsd:double) - (gnt:locus rdfs:domain gnc:phenotype) - (gnt:locus rdfs:range rdfs:Literal) - (gnt:additive rdfs:domain gnc:phenotype) - (gnt:additive rdfs:range xsd:double) - (gnt:sequence rdfs:domain gnc:phenotype) - (gnt:sequence rdfs:range xsd:integer)) - (triples (string->identifier - "trait" - (field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)" - Phenotype))) - (set rdf:type 'gnc:phenotype) - (set gnt:belongsToSet - (string->identifier - "set" (field InbredSet Name) - #:separator "" - #:proc string-capitalize-first)) - (set gnt:traitName - (let ((trait-id (field PublishXRef Id))) - (if (number? trait-id) - (number->string trait-id) - trait-id))) - (set rdfs:label - (field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)" - Phenotype))) - ;; All phenotypes have a post-publication description - (set dct:description - (sanitize-rdf-string - (field Phenotype Post_publication_description))) - ;; All phenotypes have a post-publication abbreviation - (set gnt:abbreviation (field Phenotype Post_publication_abbreviation)) - (set gnt:labCode (field Phenotype Lab_code)) - (set gnt:submitter - (sanitize-rdf-string (field Phenotype Submitter))) - (multiset dct:contributor - (string-split - (sanitize-rdf-string (field Phenotype Owner)) - #\,)) - (set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean)) - '^^xsd:double)) - (set gnt:locus (field PublishXRef Locus)) - (set gnt:LRS (annotate-field - (field ("IFNULL(PublishXRef.LRS, '')" lrs)) - '^^xsd:double)) - (set gnt:additive - (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) - '^^xsd:double)) - (set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:integer)) - (set dct:isReferencedBy - (let ((pmid (field - ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))" - pmid))) - (publication-id (field Publication Id))) - (if (string-null? pmid) - (string->identifier "unpublished" - (number->string publication-id)) - (ontology 'pubmed: pmid)))))) - - - -(dump-with-documentation - (name "Phenotypes Metadata") - (connection %connection-settings) - (table-metadata? #f) - (prefixes - '(("dct:" "<http://purl.org/dc/terms/>") - ("gn:" "<http://genenetwork.org/id/>") - ("owl:" "<http://www.w3.org/2002/07/owl#>") - ("gnc:" "<http://genenetwork.org/category/>") - ("gnt:" "<http://genenetwork.org/terms/>") - ("skos:" "<http://www.w3.org/2004/02/skos/core#>") - ("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#>") - ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>"))) - (inputs - (list - dump-phenotypes)) - (outputs - '(#:documentation "./docs/dump-phenotype.md" - #:rdf "/export/data/genenetwork-virtuoso/dump-phenotype.ttl"))) |