diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 19 |
1 files changed, 12 insertions, 7 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 5525472e..1b7cb23c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -5,15 +5,15 @@ import resource import codecs import requests -import redis -Redis = redis.StrictRedis() - from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset from db import webqtlDatabaseFunction from utility import webqtlUtil from utility import hmac +from utility.tools import GN2_BASE_URL +from utility.redis_tools import get_redis_conn +Redis = get_redis_conn() from wqflask import app @@ -135,9 +135,9 @@ class GeneralTrait(object): alias = 'Not available' if self.symbol: - human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper()) - mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize()) - other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower()) + human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) if human_response and mouse_response and other_response: alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) @@ -348,8 +348,13 @@ def jsonable_table_row(trait, dataset_name, index): def retrieve_trait_info(trait, dataset, get_qtl_info=False): assert dataset, "Dataset doesn't exist" - + if dataset.type == 'Publish': + resource_id = hmac.data_hmac("{}:{}".format(dataset.id, trait.name)) + + the_url = "http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) + trait_data = json.loads(requests.get("http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id))) + query = """ SELECT PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID, |