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-rw-r--r--wqflask/maintenance/README.md4
-rw-r--r--wqflask/maintenance/__init__.py0
-rw-r--r--wqflask/maintenance/gen_select_dataset.py26
3 files changed, 21 insertions, 9 deletions
diff --git a/wqflask/maintenance/README.md b/wqflask/maintenance/README.md
new file mode 100644
index 00000000..873eaa32
--- /dev/null
+++ b/wqflask/maintenance/README.md
@@ -0,0 +1,4 @@
+Maintenance files have been moved into a separate repository named
+*gn_extra*. See https://github.com/genenetwork/gn_extra
+
+
diff --git a/wqflask/maintenance/__init__.py b/wqflask/maintenance/__init__.py
deleted file mode 100644
index e69de29b..00000000
--- a/wqflask/maintenance/__init__.py
+++ /dev/null
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index d39bf4a5..f2f0830f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -1,7 +1,9 @@
"""Script that generates the data for the main dropdown menus on the home page
Writes out data as /static/new/javascript/dataset_menu_structure.json
-It needs to be run manually when database has been changed.
+It needs to be run manually when database has been changed. Run it as
+
+ ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
"""
@@ -37,9 +39,15 @@ from __future__ import print_function, division
#print("cdict is:", cdict)
import sys
-# import zach_settings # no hard code paths!
-# import MySQLdb
+# NEW: Note we prepend the current path - otherwise a guix instance of GN2 is used instead
+sys.path.insert(0,'./wqflask')
+# NEW: import app to avoid a circular dependency on utility.tools
+from wqflask import app
+
+from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
+
+import MySQLdb
# import simplejson as json
import urlparse
@@ -55,14 +63,13 @@ from pprint import pformat as pf
#conn = Engine.connect()
-print('ERROR: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!')
-sys.exit()
+print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!')
def parse_db_uri(db_uri):
"""Converts a database URI to the db name, host name, user name, and password"""
- parsed_uri = urlparse.urlparse(zach_settings.DB_URI)
+ parsed_uri = urlparse.urlparse(SQL_URI)
db_conn_info = dict(
db = parsed_uri.path[1:],
@@ -70,6 +77,7 @@ def parse_db_uri(db_uri):
user = parsed_uri.username,
passwd = parsed_uri.password)
+ print(db_conn_info)
return db_conn_info
@@ -258,7 +266,7 @@ def build_datasets(species, group, type_name):
def main():
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
- parse_db_uri(zach_settings.SQL_URI)
+ parse_db_uri(SQL_URI)
species = get_species()
groups = get_groups(species)
@@ -281,7 +289,7 @@ def main():
#print("data:", data)
- output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json"""
+ output_file = """./wqflask/wqflask/static/new/javascript/dataset_menu_structure.json"""
with open(output_file, 'w') as fh:
json.dump(data, fh, indent=" ", sort_keys=True)
@@ -297,6 +305,6 @@ def _test_it():
#print("build_datasets:", pf(datasets))
if __name__ == '__main__':
- Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.SQL_URI))
+ Conn = MySQLdb.Connect(**parse_db_uri(SQL_URI))
Cursor = Conn.cursor()
main()