From 849874fdfe11003f05abe5f82efde974a8c8a388 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 21 Aug 2023 14:49:55 +0300 Subject: Rename define-dump -> define-transformer Signed-off-by: Munyoki Kilyungi --- examples/dump-dataset-metadata.scm | 12 ++++++------ examples/dump-generif.scm | 6 +++--- examples/dump-genotype.scm | 2 +- examples/dump-phenotype.scm | 2 +- examples/dump-probeset-data.scm | 2 +- examples/dump-probeset.scm | 2 +- examples/dump-publication.scm | 2 +- examples/dump-species-metadata.scm | 10 +++++----- examples/dump-tissue.scm | 2 +- 9 files changed, 20 insertions(+), 20 deletions(-) (limited to 'examples') diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm index a127e57..6173201 100755 --- a/examples/dump-dataset-metadata.scm +++ b/examples/dump-dataset-metadata.scm @@ -34,7 +34,7 @@ (list first-name last-name (fix-email-id email)) "_"))) -(define-dump dump-investigators +(define-transformer dump-investigators ;; There are a few duplicate entries. We group by email to ;; deduplicate. (tables (Investigators) @@ -56,7 +56,7 @@ (set v:postal-code (field Investigators ZipCode)) (set v:country-name (field Investigators Country)))) -(define-dump dump-gene-chip +(define-transformer dump-gene-chip (tables (GeneChip (left-join Species "USING (SpeciesId)"))) (schema-triples @@ -87,7 +87,7 @@ (ontology 'geoSeries: (string-trim-both (field GeneChip GeoPlatform)))))) -(define-dump dump-info-files +(define-transformer dump-info-files (tables (InfoFiles (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name") (left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name") @@ -251,7 +251,7 @@ (field Datasets Acknowledgment))))) ;; These are phenotype datasets that don't have Infofile metadata -(define-dump dump-publishfreeze +(define-transformer dump-publishfreeze (tables (PublishFreeze (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name") (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId")) @@ -277,7 +277,7 @@ #:separator "" #:proc string-capitalize-first)))) -(define-dump dump-genofreeze +(define-transformer dump-genofreeze (tables (GenoFreeze (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name") (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId")) @@ -308,7 +308,7 @@ #:proc string-capitalize-first)))) ;; Molecular Traits are also referred to as ProbeSets -(define-dump dump-probesetfreeze +(define-transformer dump-probesetfreeze (tables (ProbeSetFreeze (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name") (left-join ProbeFreeze "USING (ProbeFreezeId)") diff --git a/examples/dump-generif.scm b/examples/dump-generif.scm index 0689f57..f754274 100755 --- a/examples/dump-generif.scm +++ b/examples/dump-generif.scm @@ -18,7 +18,7 @@ -(define-dump dump-genewiki-symbols +(define-transformer dump-genewiki-symbols (tables (GeneRIF_BASIC (left-join Species "USING (SpeciesId)")) "GROUP BY GeneId ORDER BY BINARY symbol") @@ -37,7 +37,7 @@ (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId)) #\,))))) -(define-dump dump-gn-genewiki-entries +(define-transformer dump-gn-genewiki-entries (tables (GeneRIF (left-join GeneRIF_BASIC "USING (symbol)") (left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId") @@ -101,7 +101,7 @@ (cut string-split-substring <> "::::") comments)))))) -(define-dump dump-ncbi-genewiki-entries +(define-transformer dump-ncbi-genewiki-entries (tables (GeneRIF_BASIC) "GROUP BY GeneId, comment, createtime") (schema-triples diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm index 30e7796..a055039 100755 --- a/examples/dump-genotype.scm +++ b/examples/dump-genotype.scm @@ -30,7 +30,7 @@ ["Bat (Glossophaga soricina)" "Glossophaga soricina"] [str str])) -(define-dump dump-genotypes +(define-transformer dump-genotypes (tables (Geno (left-join Species "USING (SpeciesId)"))) (schema-triples diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm index abcf140..b7ae003 100755 --- a/examples/dump-phenotype.scm +++ b/examples/dump-phenotype.scm @@ -19,7 +19,7 @@ read)) -(define-dump dump-phenotypes +(define-transformer dump-phenotypes (tables (PublishXRef (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") diff --git a/examples/dump-probeset-data.scm b/examples/dump-probeset-data.scm index 54615bc..55f3f4b 100755 --- a/examples/dump-probeset-data.scm +++ b/examples/dump-probeset-data.scm @@ -18,7 +18,7 @@ -(define-dump dump-probeset-data +(define-transformer dump-probeset-data (tables (ProbeSetXRef (left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id") (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")) diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm index c614a76..3a55506 100755 --- a/examples/dump-probeset.scm +++ b/examples/dump-probeset.scm @@ -17,7 +17,7 @@ read)) -(define-dump dump-probeset +(define-transformer dump-probeset (tables (ProbeSet (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))) (schema-triples diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm index 5b1af83..1881872 100755 --- a/examples/dump-publication.scm +++ b/examples/dump-publication.scm @@ -18,7 +18,7 @@ -(define-dump dump-publication +(define-transformer dump-publication (tables (Publication)) (triples (let ((pmid (field diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index 20b0b05..b0ac6f8 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -28,7 +28,7 @@ ["Bat (Glossophaga soricina)" "Glossophaga soricina"] [str str])) -(define-dump dump-species +(define-transformer dump-species (tables (Species)) (schema-triples (gnc:species a skos:Concept) @@ -97,7 +97,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used. !# -(define-dump dump-strain +(define-transformer dump-strain (tables (Strain (left-join Species "ON Strain.SpeciesId = Species.SpeciesId"))) (schema-triples @@ -129,7 +129,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used. (set gnt:alias (sanitize-rdf-string (field ("IF ((Strain.Alias != Strain.Name), Strain.Alias, '')" Alias)))) (set gnt:symbol (field ("IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '')" Symbol))))) -(define-dump dump-mapping-method +(define-transformer dump-mapping-method (tables (MappingMethod)) (schema-triples (gnc:mappingMethod a skos:Concept) @@ -140,7 +140,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used. (set rdfs:label (field MappingMethod Name)))) -(define-dump dump-inbred-set +(define-transformer dump-inbred-set (tables (InbredSet (left-join Species "ON InbredSet.SpeciesId=Species.Id") (left-join MappingMethod @@ -189,7 +189,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used. molecularTrait)) "||"))))) -(define-dump dump-avg-method +(define-transformer dump-avg-method ;; The Name and Normalization fields seem to be the same. Dump only ;; the Name field. (tables (AvgMethod)) diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm index f11b8b4..3658a26 100755 --- a/examples/dump-tissue.scm +++ b/examples/dump-tissue.scm @@ -18,7 +18,7 @@ -(define-dump dump-tissue +(define-transformer dump-tissue ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID ;; and BIRN_lex_Name are mostly NULL. (tables (Tissue)) -- cgit v1.2.3