diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/genotype-datasets.scm | 6 | ||||
| -rwxr-xr-x | examples/phenotype-datasets.scm | 4 | ||||
| -rwxr-xr-x | examples/phenotype.scm | 2 | ||||
| -rwxr-xr-x | examples/probesets-experiment-metadata.scm | 3 |
4 files changed, 8 insertions, 7 deletions
diff --git a/examples/genotype-datasets.scm b/examples/genotype-datasets.scm index ebe2349..38d524b 100755 --- a/examples/genotype-datasets.scm +++ b/examples/genotype-datasets.scm @@ -18,7 +18,7 @@ (tables (Species (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id") (inner-join GenoFreeze "ON GenoFreeze.InbredSetId = InbredSet.Id")) - "WHERE GenoFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, GenoFreeze.ShortName") + "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND Species.Name != 'monkey' GROUP BY Species.Name, GenoFreeze.ShortName") (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") (multiset gnt:has_genotype_data (map (cut string->identifier "dataset" <> #:separator "_") @@ -31,7 +31,7 @@ (tables (GenoFreeze (inner-join InbredSet "ON InbredSet.Id = GenoFreeze.InbredSetId") (inner-join Species "ON InbredSet.SpeciesId = Species.Id")) - "WHERE GenoFreeze.public > 0 AND Species.Name != 'monkey'") + "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND Species.Name != 'monkey'") (triples (string->identifier "dataset" (field GenoFreeze Name) #:separator "_") (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")) (set dct:created (annotate-field (field GenoFreeze CreateTime) '^^xsd:datetime)))) @@ -41,7 +41,7 @@ (inner-join InbredSet "ON InbredSet.Id = GenoFreeze.InbredSetId") (inner-join Species "ON InbredSet.SpeciesId = Species.Id") (inner-join Geno "ON Geno.SpeciesId = Species.Id")) - "WHERE GenoFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY GenoFreeze.Name") + "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND Species.Name != 'monkey' GROUP BY GenoFreeze.Name") (triples (string->identifier "dataset" (field GenoFreeze Name) #:separator "_") (set gnt:has_marker_count (string->symbol diff --git a/examples/phenotype-datasets.scm b/examples/phenotype-datasets.scm index c8657fc..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 "_") @@ -34,7 +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))) diff --git a/examples/phenotype.scm b/examples/phenotype.scm index c2564b6..57fd2c5 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -71,7 +71,7 @@ (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id") (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) - "WHERE InbredSet.public > 0") + "WHERE InbredSet.public > 0 AND PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1") (triples (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))) diff --git a/examples/probesets-experiment-metadata.scm b/examples/probesets-experiment-metadata.scm index e019928..b15f7e9 100755 --- a/examples/probesets-experiment-metadata.scm +++ b/examples/probesets-experiment-metadata.scm @@ -16,7 +16,8 @@ (define-transformer probesetxref->metadata (tables (ProbeSetXRef (inner-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id") - (inner-join ProbeSet "ON ProbeSet.Id = ProbeSetXRef.ProbeSetId"))) + (inner-join ProbeSet "ON ProbeSet.Id = ProbeSetXRef.ProbeSetId")) + "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1") (triples (string->identifier "probeset_data" (uri-encode |