diff options
| -rw-r--r-- | wqflask/wqflask/api/router.py | 46 |
1 files changed, 34 insertions, 12 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 8ec93e48..e2e91d70 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -209,6 +209,8 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): where_statement = """ WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.TissueId = Tissue.Id AND + ProbeSetFreeze.public > 0 AND + ProbeSetFreeze.confidentiality < 1 AND """ if dataset_name.isdigit(): where_statement += """ @@ -249,6 +251,8 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): WHERE PublishXRef.InbredSetId = InbredSet.Id AND PublishXRef.PhenotypeId = Phenotype.Id AND PublishXRef.PublicationId = Publication.Id AND + PublishFreeze.public > 0 AND + PublishFreeze.confidentiality < 1 AND InbredSet.Name = "{0}" AND PublishXRef.Id = "{1}" """.format(group_name, dataset_name) @@ -330,10 +334,13 @@ def fetch_traits(dataset_name, file_format = "json"): ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.h2 FROM - ProbeSet, ProbeSetXRef + ProbeSet, ProbeSetXRef, ProbeSetFreeze WHERE ProbeSetXRef.ProbeSetFreezeId = "{0}" AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetFreeze.public > 0 AND + ProbeSetFreeze.confidentiality < 1 ORDER BY ProbeSet.Id """ @@ -344,10 +351,13 @@ def fetch_traits(dataset_name, file_format = "json"): SELECT Geno.Id, Geno.Name, Geno.Marker_Name, Geno.Chr, Geno.Mb, Geno.Sequence, Geno.Source FROM - Geno, GenoXRef + Geno, GenoXRef, GenoFreeze WHERE GenoXRef.GenoFreezeId = "{0}" AND - GenoXRef.GenoId = Geno.Id + GenoXRef.GenoId = Geno.Id AND + GenoXRef.GenoFreezeId = GenoFreeze.Id AND + GenoFreeze.public > 0 AND + GenoFreeze.confidentiality < 1 ORDER BY Geno.Id """ @@ -358,9 +368,12 @@ def fetch_traits(dataset_name, file_format = "json"): SELECT PublishXRef.Id, PublishXRef.PhenotypeId, PublishXRef.PublicationId, PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive, PublishXRef.Sequence FROM - PublishXRef + PublishXRef, PublishFreeze WHERE - PublishXRef.InbredSetId = {0} + PublishXRef.InbredSetId = {0} AND + PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND + PublishFreeze.public > 0 AND + PublishFreeze.confidentiality < 1 ORDER BY PublishXRef.Id """ @@ -422,14 +435,17 @@ def all_sample_data(dataset_name, file_format = "csv"): SELECT Strain.Name, Strain.Name2, ProbeSetData.value, ProbeSetData.Id, ProbeSetSE.error FROM - (ProbeSetData, Strain, ProbeSetXRef) + (ProbeSetData, Strain, ProbeSetXRef, ProbeSetFreeze) LEFT JOIN ProbeSetSE ON (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) WHERE ProbeSetXRef.ProbeSetFreezeId = "{0}" AND ProbeSetXRef.ProbeSetId = "{1}" AND ProbeSetXRef.DataId = ProbeSetData.Id AND - ProbeSetData.StrainId = Strain.Id + ProbeSetData.StrainId = Strain.Id AND + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetFreeze.public > 0 AND + ProbeSetFreeze.confidentiality < 1 ORDER BY Strain.Name """ @@ -438,14 +454,17 @@ def all_sample_data(dataset_name, file_format = "csv"): SELECT Strain.Name, Strain.Name2, GenoData.value, GenoData.Id, GenoSE.error FROM - (GenoData, Strain, GenoXRef) + (GenoData, Strain, GenoXRef, GenoFreeze) LEFT JOIN GenoSE ON (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) WHERE GenoXRef.GenoFreezeId = "{0}" AND GenoXRef.GenoId = "{1}" AND GenoXRef.DataId = GenoData.Id AND - GenoData.StrainId = Strain.Id + GenoData.StrainId = Strain.Id AND + GenoXRef.GenoFreezeId = GenoFreeze.Id AND + GenoFreeze.public > 0 AND + GenoFreeze.confidentiality < 1 ORDER BY Strain.Name """ @@ -454,7 +473,7 @@ def all_sample_data(dataset_name, file_format = "csv"): SELECT Strain.Name, Strain.Name2, PublishData.value, PublishData.Id, PublishSE.error, NStrain.count FROM - (PublishData, Strain, PublishXRef) + (PublishData, Strain, PublishXRef, PublishFreeze) LEFT JOIN PublishSE ON (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) LEFT JOIN NStrain ON @@ -464,7 +483,10 @@ def all_sample_data(dataset_name, file_format = "csv"): PublishXRef.InbredSetId = "{0}" AND PublishXRef.PhenotypeId = "{1}" AND PublishData.Id = PublishXRef.DataId AND - PublishData.StrainId = Strain.Id + PublishData.StrainId = Strain.Id AND + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishFreeze.public > 0 AND + PublishFreeze.confidentiality < 1 ORDER BY Strain.Name """ |