diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/data_set.py | 2 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 1 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 26 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 1 |
4 files changed, 19 insertions, 11 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1b4e1195..6cd3c8e6 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -91,7 +91,7 @@ Publish or ProbeSet. E.g. if USE_GN_SERVER: data = menu_main() else: - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" + file_name = "wqflask/wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index f76d8140..8c67a6fd 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -80,4 +80,3 @@ PORTADDR = "http://50.16.251.170" INFOPAGEHREF = '/dbdoc/%s.html' CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' SCRIPTFILE = 'main.py' - diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index d39bf4a5..5c25c15b 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 + + python 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() diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index bb8241f5..2c8cc5c5 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -3,6 +3,7 @@ import os import sys + from wqflask import app # Use the standard logger here to avoid a circular dependency |