diff options
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 55 | ||||
| l--------- | wqflask/maintenance/our_settings.py | 1 |
2 files changed, 42 insertions, 14 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 4c544192..acf21ed8 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -29,25 +29,47 @@ 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 -from pprint import pformat as pf -from base import webqtlConfig +#import sqlalchemy as sa + +from pprint import pformat as pf +#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI) # 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() + +#conn = Engine.connect() + + + + + +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(): @@ -100,8 +122,8 @@ 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() @@ -140,14 +162,17 @@ 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""" + + parse_db_uri(our_settings.DB_URI) + species = get_species() groups = get_groups(species) types = get_types(groups) @@ -182,5 +207,7 @@ 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() diff --git a/wqflask/maintenance/our_settings.py b/wqflask/maintenance/our_settings.py new file mode 120000 index 00000000..14efe407 --- /dev/null +++ b/wqflask/maintenance/our_settings.py @@ -0,0 +1 @@ +../../../zach_settings.py
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