diff options
| -rwxr-xr-x | examples/phenotype-datasets.scm | 54 | ||||
| -rwxr-xr-x | examples/phenotype.scm | 51 |
2 files changed, 52 insertions, 53 deletions
diff --git a/examples/phenotype-datasets.scm b/examples/phenotype-datasets.scm index 410178a..4819627 100755 --- a/examples/phenotype-datasets.scm +++ b/examples/phenotype-datasets.scm @@ -15,13 +15,17 @@ (define-transformer gn:set->gn:dataset - (tables (Datasets - (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") - (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") + (tables (Species + (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id") (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")) - "WHERE PublishFreeze.public > 0 GROUP BY Datasets.DatasetId") + "WHERE PublishFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, PublishFreeze.ShortName") (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") - (set gnt:has_phenotype_data (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")))) + (multiset gnt:has_phenotype_data + (map (cut string->identifier "dataset" <> #:separator "_") + (string-split + (field ("GROUP_CONCAT(PublishFreeze.Name SEPARATOR ',')" + dataset_name)) + #\,))))) (define-transformer gn:dataset->gn:set (tables (Datasets @@ -32,6 +36,40 @@ (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_") (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) +(define-transformer gn:dataset->metadata + (tables (PublishXRef + (inner-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") + (inner-join Species "ON InbredSet.SpeciesId = Species.Id") + (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id") + (inner-join Publication "ON Publication.Id = PublishXRef.PublicationId") + (inner-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) + "WHERE InbredSet.public > 0 GROUP BY Species.Name, PublishFreeze.Name") + (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_") + (set dct:created (annotate-field (field PublishFreeze CreateTime) '^^xsd:datetime)) + (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + +(define-transformer gn:dataset->gn:trait + (tables (PublishXRef + (inner-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") + (inner-join Species "ON InbredSet.SpeciesId = Species.Id") + (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id") + (inner-join Publication "ON Publication.Id = PublishXRef.PublicationId") + (inner-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) + "WHERE InbredSet.public > 0") + (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_") + (set gnt:has_phenotype_trait + (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation))) + (pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation))) + (post-desc (blank-p (field Phenotype Post_publication_description))) + (pre-desc (blank-p (field Phenotype Post_publication_description)))) + (string->identifier + "trait" + (format #f "~a_~a" (field PublishFreeze Name) + (or post-abbrev pre-abbrev post-desc pre-desc)) + #:separator "_"))) + (set dct:created (annotate-field (field PublishFreeze CreateTime) '^^xsd:datetime)) + (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + (let* ((option-spec '((settings (single-char #\s) (value #t)) @@ -61,7 +99,11 @@ ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>") ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) (inputs - (list gn:set->gn:dataset gn:dataset->gn:set)) + (list + gn:set->gn:dataset + gn:dataset->gn:set + gn:dataset->metadata + gn:dataset->gn:trait)) (outputs `(#:documentation ,documentation #:rdf ,output)))) diff --git a/examples/phenotype.scm b/examples/phenotype.scm index 43e92f1..834ff5a 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -12,55 +12,14 @@ (transform sql) (transform triples) (transform special-forms)) + + -(define-transformer gn:set->gn:dataset - (tables (Species - (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id") - (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")) - "WHERE PublishFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, PublishFreeze.ShortName") - (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") - (multiset gnt:has_phenotype_data - (map (cut string->identifier "dataset" <> #:separator "_") - (string-split - (field ("GROUP_CONCAT(PublishFreeze.Name SEPARATOR ',')" - dataset_name)) - #\,))))) -(define-transformer gn:dataset->metadata - (tables (PublishXRef - (inner-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") - (inner-join Species "ON InbredSet.SpeciesId = Species.Id") - (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id") - (inner-join Publication "ON Publication.Id = PublishXRef.PublicationId") - (inner-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) - "WHERE InbredSet.public > 0 GROUP BY Species.Name, PublishFreeze.Name") - (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_") - (set dct:created (annotate-field (field PublishFreeze CreateTime) '^^xsd:datetime)) - (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) -(define-transformer gn:dataset->gn:trait - (tables (PublishXRef - (inner-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") - (inner-join Species "ON InbredSet.SpeciesId = Species.Id") - (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id") - (inner-join Publication "ON Publication.Id = PublishXRef.PublicationId") - (inner-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) - "WHERE InbredSet.public > 0") - (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_") - (set gnt:has_phenotype_trait - (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation))) - (pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation))) - (post-desc (blank-p (field Phenotype Post_publication_description))) - (pre-desc (blank-p (field Phenotype Post_publication_description)))) - (string->identifier - "trait" - (format #f "~a_~a" (field PublishFreeze Name) - (or post-abbrev pre-abbrev post-desc pre-desc)) - #:separator "_"))) - (set dct:created (annotate-field (field PublishFreeze CreateTime) '^^xsd:datetime)) - (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + (define-transformer gnc:phenotype->gn:phenotype (tables (Phenotype)) @@ -196,9 +155,7 @@ ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>") ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>"))) (inputs - (list gn:dataset->metadata - gn:dataset->gn:trait - gnc:phenotype->gn:phenotype + (list gnc:phenotype->gn:phenotype gn:phenotype->metadata gn:trait->gn:phenotype)) (outputs |