diff options
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 33 |
1 files changed, 24 insertions, 9 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 9224b884..4c544192 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -1,3 +1,10 @@ +"""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. + +""" + # Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it @@ -13,16 +20,13 @@ # This program is available from Source Forge: at GeneNetwork Project # (sourceforge.net/projects/genenetwork/). # -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# Contact Drs. Robert W. Williams +# at rwilliams@uthsc.edu # # # # This module is used by GeneNetwork project (www.genenetwork.org) -# This script is to generate the data for the main menus on the home page -# It needs to be run manually when database has been changed . - from __future__ import print_function, division import sys @@ -39,7 +43,8 @@ from base import webqtlConfig # build MySql database connection -Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, +Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, + host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD) Cursor = Con.cursor() @@ -82,6 +87,12 @@ def get_types(groups): def build_types(species, group): + """Fetches tissues + + Gets the tissues with data for this species/group + (all types except phenotype/genotype are tissues) + + """ Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and @@ -101,12 +112,13 @@ def get_datasets(types): datasets[species] = {} for group, type_list in group_dict.iteritems(): datasets[species][group] = {} - for type_name, type_full_name in type_list: + for type_name, _type_full_name in type_list: datasets[species][group][type_name] = build_datasets(species, group, type_name) return datasets def build_datasets(species, group, type_name): + """Gets dataset names from database""" dataset_text = dataset_value = None if type_name == "Phenotypes": dataset_value = "%sPublish" % group @@ -135,6 +147,7 @@ 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""" species = get_species() groups = get_groups(species) types = get_types(groups) @@ -154,14 +167,16 @@ def main(): datasets=datasets, ) - output_file = """../wqflask/static/new/javascript/dataset_menu_structure""" + output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" with open(output_file, 'w') as fh: json.dump(data, fh, indent=" ", sort_keys=True) print("\nWrote file to:", output_file) -def test_it(): + +def _test_it(): + """Used for internal testing only""" types = build_types("Mouse", "BXD") print("build_types:", pf(types)) datasets = build_datasets("Mouse", "BXD", "Hippocampus") |