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authorBonfaceKilz2020-07-27 19:11:11 +0300
committerBonfaceKilz2020-07-27 19:11:11 +0300
commitfea8444fb7b0224fd44711853904822ee8b43f4f (patch)
treecd26735b2df18830cb1ccbddf6e1de9d4aee1955 /wqflask
parent79b8cf45c1c40b9c20278762b6e8f587a2820b43 (diff)
downloadgenenetwork2-fea8444fb7b0224fd44711853904822ee8b43f4f.tar.gz
Abstract away redundant code into set_dataset_key method
* wqflask/base/data_set.py (Dataset): - Add set_dataset_key - Remove __call__ method
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/data_set.py109
1 files changed, 47 insertions, 62 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index bce94aa8..cfba9104 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -117,71 +117,56 @@ Publish or ProbeSet. E.g.
self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
- # Set LOG_LEVEL_DEBUG=5 to see the following:
- logger.debugf(5, "datasets", self.datasets)
+ def set_dataset_key(self, t, name):
+ """If name is not in the object's dataset dictionary, set it, and update
+ dataset_structure in Redis
+
+ args:
+ t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
+ 'other_pheno', 'geno'
+ name: The name of the key to inserted in the datasets dictionary
+
+ """
+ sql_query_mapping = {
+ 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
+ """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
+ 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
+ """FROM InfoFiles, PublishFreeze, InbredSet """ +
+ """WHERE InbredSet.Name = '{}' AND """ +
+ """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
+ """InfoFiles.InfoPageName = PublishFreeze.Name"""),
+ 'other_pheno': ("""SELECT PublishFreeze.Name """ +
+ """FROM PublishFreeze, InbredSet """ +
+ """WHERE InbredSet.Name = '{}' AND """ +
+ """PublishFreeze.InbredSetId = InbredSet.Id"""),
+ 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
+ """GenoFreeze.Name = "{}" """)
+ }
+
+ dataset_name_mapping = {
+ "mrna_expr": "ProbeSet",
+ "pheno": "Publish",
+ "other_pheno": "Publish",
+ "geno": "Geno",
+ }
+
+ if t in ['pheno', 'other_pheno']:
+ name = name.replace("Publish", "")
+ if bool(len(g.db.execute(sql_query_mapping[t].format(name)))):
+ self.datasets[name] = dataset_name_mapping[t]
+ self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ return True
+
+ return None
def __call__(self, 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(mrna_expr_query).fetchall()
- if len(results):
- self.datasets[name] = "ProbeSet"
- redis_instance.set("dataset_structure", json.dumps(self.datasets))
- 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"
- redis_instance.set("dataset_structure", json.dumps(self.datasets))
- 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"
- redis_instance.set("dataset_structure", json.dumps(self.datasets))
- return self.datasets[name]
-
- geno_query = """
- SELECT
- GenoFreeze.Id
- FROM
- GenoFreeze
- WHERE
- GenoFreeze.Name = "{0}"
- """.format(name)
-
- results = g.db.execute(geno_query).fetchall()
- if len(results):
- self.datasets[name] = "Geno"
- self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
- return self.datasets[name]
-
- # ZS: It shouldn't ever reach this
- return None
- else:
- return self.datasets[name]
+ for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
+ # This has side-effects, with the end result being a truth-y value
+ if(self.set_dataset_key(t, name)):
+ break
+ return self.datasets.get(name, None) # Return None if name has not been set
# Do the intensive work at startup one time only