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| author | zsloan | 2024-07-08 19:18:53 +0000 |
|---|---|---|
| committer | zsloan | 2024-07-12 20:09:57 +0000 |
| commit | 4825a108ef1bb572537c00e43cd915ba09ffe207 (patch) | |
| tree | a6af645577fbed130d5afe1ff249b55473710b08 | |
| parent | 081649943d14ef1ae2d6f635e9daf56c88a882c9 (diff) | |
| download | genenetwork2-4825a108ef1bb572537c00e43cd915ba09ffe207.tar.gz | |
Add Peak Chr and Peak Mb columns to ProbeSet export in the GN2 REST API
| -rw-r--r-- | gn2/wqflask/api/router.py | 33 |
1 files changed, 19 insertions, 14 deletions
diff --git a/gn2/wqflask/api/router.py b/gn2/wqflask/api/router.py index bcd08e8d..e9b70919 100644 --- a/gn2/wqflask/api/router.py +++ b/gn2/wqflask/api/router.py @@ -379,23 +379,28 @@ def fetch_traits(dataset_name, file_format="json"): if len(trait_ids) > 0: if data_type == "ProbeSet": query = """ - SELECT - 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, ProbeSetFreeze + SELECT DISTINCT + 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`, + Geno.`Chr`, Geno.`Mb` + FROM + Species + INNER JOIN InbredSet ON InbredSet.`SpeciesId`= Species.`Id` + INNER JOIN ProbeFreeze ON ProbeFreeze.`InbredSetId` = InbredSet.`Id` + INNER JOIN Tissue ON ProbeFreeze.`TissueId` = Tissue.`Id` + INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.`ProbeFreezeId` = ProbeFreeze.`Id` + INNER JOIN ProbeSetXRef ON ProbeSetXRef.`ProbeSetFreezeId` = ProbeSetFreeze.`Id` + INNER JOIN ProbeSet ON ProbeSet.`Id` = ProbeSetXRef.`ProbeSetId` + LEFT JOIN Geno ON ProbeSetXRef.`Locus` = Geno.`Name` AND Geno.`SpeciesId` = Species.`Id` WHERE - ProbeSetXRef.ProbeSetFreezeId = "{0}" AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.public > 0 AND - ProbeSetFreeze.confidentiality < 1 + ProbeSetXRef.ProbeSetFreezeId = "{0}" ORDER BY - ProbeSet.Id - """ + ProbeSet.Id""" - field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", - "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] + field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", + "SE", "Locus", "LRS", "P-Value", "Additive", "h2", "Peak Chr", "Peak Mb"] elif data_type == "Geno": query = """ SELECT |