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authorPjotr Prins2016-06-23 10:27:18 +0000
committerPjotr Prins2016-06-23 10:27:18 +0000
commit8044e04c171d972fa64c510320c781360b823c07 (patch)
tree74c92a0c62e04366a40707a54ee7d6ef11e1969a /wqflask
parent0a6c114a20d2b02476949511773ad32e591d7d80 (diff)
downloadgenenetwork2-8044e04c171d972fa64c510320c781360b823c07.tar.gz
Removed dependency on dataset_menu_structure.json
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/data_set.py32
-rw-r--r--wqflask/wqflask/search_results.py10
2 files changed, 28 insertions, 14 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 02018dd3..321dbf3f 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -50,7 +50,9 @@ from maintenance import get_group_samplelists
from MySQLdb import escape_string as escape
from pprint import pformat as pf
+from db.gn_server import menu_main
+from utility.tools import USE_GN_SERVER
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -61,8 +63,7 @@ DS_NAME_MAP = {}
def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
-
- logger.debug("dataset_type is:", dataset_type)
+ logger.debug("dataset_type", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
@@ -71,12 +72,28 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
class Dataset_Types(object):
def __init__(self):
+ """Create a dictionary of samples where the value is set to Geno,
+Publish or ProbeSet. E.g.
+
+ {'AD-cases-controls-MyersGeno': 'Geno',
+ 'AD-cases-controls-MyersPublish': 'Publish',
+ 'AKXDGeno': 'Geno',
+ 'AXBXAGeno': 'Geno',
+ 'AXBXAPublish': 'Publish',
+ 'Aging-Brain-UCIPublish': 'Publish',
+ 'All Phenotypes': 'Publish',
+ 'B139_K_1206_M': 'ProbeSet',
+ 'B139_K_1206_R': 'ProbeSet' ...
+
+ """
self.datasets = {}
- file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
- with open(file_name, 'r') as fh:
- data = json.load(fh)
+ if USE_GN_SERVER:
+ data = menu_main()
+ else:
+ file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
+ with open(file_name, 'r') as fh:
+ data = json.load(fh)
- logger.debug("*" * 70)
for species in data['datasets']:
for group in data['datasets'][species]:
for dataset_type in data['datasets'][species][group]:
@@ -88,7 +105,8 @@ class Dataset_Types(object):
new_type = "Geno"
else:
new_type = "ProbeSet"
- self.datasets[short_dataset_name] = new_type
+ self.datasets[short_dataset_name] = new_type
+ logger.info("datasets",self.datasets)
def __call__(self, name):
return self.datasets[name]
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index c1b8683e..b1e7b8db 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -1,8 +1,5 @@
-from __future__ import absolute_import, print_function, division
+# from __future__ import absolute_import, print_function, division
-from wqflask import app
-
-from flask import render_template
import os
import cPickle
@@ -18,9 +15,6 @@ from pprint import pformat as pf
import json
-# from flask import Flask, g
-
-# from utility.benchmark import Bench
from base.data_set import create_dataset
from base.trait import GeneralTrait
from wqflask import parser
@@ -28,6 +22,8 @@ from wqflask import do_search
from utility import webqtlUtil,tools
from db import webqtlDatabaseFunction
+from flask import render_template
+
from utility import formatting
from utility.logger import getLogger