diff options
Diffstat (limited to 'examples/phenotype-datasets.scm')
| -rwxr-xr-x | examples/phenotype-datasets.scm | 27 |
1 files changed, 2 insertions, 25 deletions
diff --git a/examples/phenotype-datasets.scm b/examples/phenotype-datasets.scm index 4819627..c005621 100755 --- a/examples/phenotype-datasets.scm +++ b/examples/phenotype-datasets.scm @@ -18,7 +18,7 @@ (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") + "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 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 "_") @@ -27,27 +27,6 @@ dataset_name)) #\,))))) -(define-transformer gn:dataset->gn:set - (tables (Datasets - (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") - (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") - (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")) - "WHERE PublishFreeze.public > 0 GROUP BY Datasets.DatasetId") - (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") @@ -55,7 +34,7 @@ (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") + "WHERE InbredSet.public > 0 AND PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1") (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_") (set gnt:has_phenotype_trait (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation))) @@ -101,8 +80,6 @@ (inputs (list gn:set->gn:dataset - gn:dataset->gn:set - gn:dataset->metadata gn:dataset->gn:trait)) (outputs `(#:documentation ,documentation |