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| author | zsloan | 2022-12-01 20:52:59 +0000 |
|---|---|---|
| committer | zsloan | 2022-12-01 20:52:59 +0000 |
| commit | 613656943b3962f2763ca376c8dbeb8edc6b969a (patch) | |
| tree | 2eb20154fd96fbede43bc1e09a747b939d002334 | |
| parent | 203349bdf21dc43b89c9776c57ee545651f5460f (diff) | |
| download | genenetwork2-613656943b3962f2763ca376c8dbeb8edc6b969a.tar.gz | |
Change API Phenotype query to get other fields, including Locus position
| -rw-r--r-- | wqflask/wqflask/api/router.py | 38 |
1 files changed, 24 insertions, 14 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 2c1c2614..bae1d129 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -416,22 +416,32 @@ def fetch_traits(dataset_name, file_format="json"): field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"] else: - query = """ - SELECT - PublishXRef.Id, PublishXRef.PhenotypeId, PublishXRef.PublicationId, PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive, PublishXRef.Sequence - FROM - PublishXRef, PublishFreeze - WHERE - PublishXRef.InbredSetId = {0} AND - PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND - PublishFreeze.public > 0 AND - PublishFreeze.confidentiality < 1 + query = """SELECT PublishXRef.Id, + Publication.`Authors`, + Publication.`Year`, + Publication.`PubMed_ID`, + PublishXRef.`mean`, + PublishXRef.`LRS`, + PublishXRef.`additive`, + PublishXRef.`Locus`, + CONCAT('Chr', Geno.`Chr`, ': ', Geno.`Mb`) + FROM Species + INNER JOIN InbredSet ON InbredSet.`SpeciesId` = Species.`Id` + INNER JOIN PublishXRef ON PublishXRef.`InbredSetId` = InbredSet.`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` + LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id + WHERE + PublishXRef.InbredSetId = {0} AND + PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND + PublishFreeze.public > 0 AND + PublishFreeze.confidentiality < 1 ORDER BY - PublishXRef.Id - """ + PublishXRef.Id""" - field_list = ["Id", "PhenotypeId", "PublicationId", - "Locus", "LRS", "Additive", "Sequence"] + field_list = ["Id", "Authors", "Year", "PubMedID", "Mean", + "LRS", "Additive", "Locus", "Position"] if 'limit_to' in request.args: limit_number = request.args['limit_to'] |