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authorzsloan2019-11-21 14:55:50 -0600
committerzsloan2019-11-21 14:55:50 -0600
commit8427ddfd7b60d74f4be3a453dd0b21ce7bfdb6f3 (patch)
tree4a036c0613cce54b067476e4f1c6a881c6ff4bb2 /wqflask/base/data_set.py
parent74e81163fb3c2418b88f6d4fbb99760c63a3fea6 (diff)
downloadgenenetwork2-8427ddfd7b60d74f4be3a453dd0b21ce7bfdb6f3.tar.gz
Added 3-letter codes to unpublished phenotype traits and fixed issue with ordering phenotype results from searches
Diffstat (limited to 'wqflask/base/data_set.py')
-rw-r--r--wqflask/base/data_set.py19
1 files changed, 9 insertions, 10 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f58367ca..6e07e383 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -26,6 +26,7 @@ import collections
import codecs
import json
+import requests
import gzip
import cPickle as pickle
import itertools
@@ -63,7 +64,7 @@ logger = getLogger(__name__ )
# Each subclass will add to this
DS_NAME_MAP = {}
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
+def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
logger.debug("dataset_type", dataset_type)
@@ -77,7 +78,7 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, gro
class Dataset_Types(object):
- def __init__(self):
+ def __init__(self, rebuild=False):
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
@@ -93,8 +94,10 @@ Publish or ProbeSet. E.g.
"""
self.datasets = {}
- if USE_GN_SERVER:
- data = gen_menu.gen_dropdown_json()
+ if rebuild: #ZS: May make this the only option
+ data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content)
+ logger.debug("THE DATA:", data)
+ #data = gen_menu.gen_dropdown_json()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
with open(file_name, 'r') as fh:
@@ -119,12 +122,8 @@ Publish or ProbeSet. E.g.
def __call__(self, name):
return self.datasets[name]
-def rebuild_dataset_ob():
- Dataset_Getter = Dataset_Types()
- return Dataset_Getter
-
# Do the intensive work at startup one time only
-Dataset_Getter = rebuild_dataset_ob()
+Dataset_Getter = Dataset_Types()
def create_datasets_list():
if USE_REDIS:
@@ -705,7 +704,7 @@ class PhenotypeDataSet(DataSet):
'PublishXRef.Id']
# Figure out what display_fields is
- self.display_fields = ['name',
+ self.display_fields = ['name', 'group_code',
'pubmed_id',
'pre_publication_description',
'post_publication_description',