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authorzsloan2020-04-24 12:58:39 -0500
committerzsloan2020-04-24 12:58:39 -0500
commit2a119affad1830d5a693860279ca2aa2897d84ef (patch)
tree3f79f6297670f54fabebb8aa49a89a6f6a525d56 /wqflask/base
parent79d935dfa02de7507103b45266a61264cfe8f735 (diff)
downloadgenenetwork2-2a119affad1830d5a693860279ca2aa2897d84ef.tar.gz
Made a fix that should prevent the issue where new datasets cause an error when they're in search results
Diffstat (limited to 'wqflask/base')
-rw-r--r--wqflask/base/data_set.py62
1 files changed, 59 insertions, 3 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index ebf3f021..fae62875 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -67,7 +67,6 @@ DS_NAME_MAP = {}
def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
- logger.debug("dataset_type", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
@@ -96,7 +95,6 @@ Publish or ProbeSet. E.g.
self.datasets = {}
if rebuild: #ZS: May make this the only option
data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content)
- logger.debug("THE DATA:", data)
#data = gen_menu.gen_dropdown_json()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
@@ -120,7 +118,65 @@ Publish or ProbeSet. E.g.
logger.debugf(5, "datasets",self.datasets)
def __call__(self, name):
- return self.datasets[name]
+ if name not in self.datasets:
+ mrna_expr_query = """
+ SELECT
+ ProbeSetFreeze.Id
+ FROM
+ ProbeSetFreeze
+ WHERE
+ ProbeSetFreeze.Name = "{0}"
+ """.format(name)
+
+ results = g.db.execute(geno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "ProbeSet"
+ return self.datasets[name]
+
+ group_name = name.replace("Publish", "")
+
+ pheno_query = """SELECT InfoFiles.GN_AccesionId
+ FROM InfoFiles, PublishFreeze, InbredSet
+ WHERE InbredSet.Name = '{0}' AND
+ PublishFreeze.InbredSetId = InbredSet.Id AND
+ InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name)
+
+ results = g.db.execute(pheno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "Publish"
+ return self.datasets[name]
+
+ #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
+ other_pheno_query = """SELECT PublishFreeze.Name
+ FROM PublishFreeze, InbredSet
+ WHERE InbredSet.Name = '{}' AND
+ PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name)
+
+ results = g.db.execute(other_pheno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "Publish"
+ return self.datasets[name]
+
+ geno_query = """
+ SELECT
+ GenoFreezeId
+ FROM
+ GenoFreeze
+ WHERE
+ GenoFreeze.Name = "{0}"
+ {1}
+ """.format(name)
+
+ results = g.db.execute(geno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "Geno"
+ return self.datasets[name]
+
+ #ZS: It shouldn't ever reach this
+ return None
+
+ else:
+ return self.datasets[name]
# Do the intensive work at startup one time only
Dataset_Getter = Dataset_Types()