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path: root/wqflask/maintenance/gen_select_dataset.py
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-rw-r--r--wqflask/maintenance/gen_select_dataset.py50
1 files changed, 36 insertions, 14 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index b6bf5bfd..d653fd2d 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -29,24 +29,38 @@ It needs to be run manually when database has been changed.
from __future__ import print_function, division
-import sys
+#from flask import config
+#
+#cdict = {}
+#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS')
+#print("cdict is:", cdict)
-sys.path.insert(0, "..")
+import our_settings
import MySQLdb
import simplejson as json
+import urlparse
+
+
+#import sqlalchemy as sa
from pprint import pformat as pf
-from base import webqtlConfig
-# build MySql database connection
-Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,
- host=webqtlConfig.MYSQL_SERVER,
- user=webqtlConfig.DB_USER,
- passwd=webqtlConfig.DB_PASSWD)
-Cursor = Con.cursor()
+def parse_db_uri(db_uri):
+ """Converts a database URI to the db name, host name, user name, and password"""
+
+ parsed_uri = urlparse.urlparse(our_settings.DB_URI)
+
+ db_conn_info = dict(
+ db = parsed_uri.path[1:],
+ host = parsed_uri.hostname,
+ user = parsed_uri.username,
+ passwd = parsed_uri.password)
+
+ return db_conn_info
+
def get_species():
@@ -99,8 +113,8 @@ def build_types(species, group):
ProbeFreeze.TissueId = Tissue.Id and
ProbeFreeze.InbredSetId = InbredSet.Id and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
- ProbeSetFreeze.public > %s
- order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH))
+ ProbeSetFreeze.public > 0
+ order by Tissue.Name""", (species, group))
return Cursor.fetchall()
@@ -139,15 +153,21 @@ def build_datasets(species, group, type_name):
InbredSet.Name = %s and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s
and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId =
- InbredSet.Id and ProbeSetFreeze.public > %s order by
+ InbredSet.Id and ProbeSetFreeze.public > 0 order by
ProbeSetFreeze.CreateTime desc""", (
- species, group, type_name, webqtlConfig.PUBLICTHRESH))
+ species, group, type_name))
return Cursor.fetchall()
def main():
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
+<<<<<<< HEAD
+
+ parse_db_uri(our_settings.DB_URI)
+
+=======
+>>>>>>> 1a3a456eb7635337a966913f2e2e75c8a89bb92e
species = get_species()
groups = get_groups(species)
types = get_types(groups)
@@ -182,5 +202,7 @@ def _test_it():
datasets = build_datasets("Mouse", "BXD", "Hippocampus")
print("build_datasets:", pf(datasets))
-if __name__ == '__main__':
+if __name__ == '__main__':
+ Conn = MySQLdb.Connect(**parse_db_uri(our_settings.DB_URI))
+ Cursor = Conn.cursor()
main()