From cf49e1ea02568fa9b31505c08e68baf844703c15 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 3 Mar 2020 15:37:19 -0600 Subject: Forgot to replace code referring to hmac function user_manager --- wqflask/base/trait.py | 11 +++++------ wqflask/wqflask/correlation/show_corr_results.py | 5 ++--- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 1 - wqflask/wqflask/gsearch.py | 6 +++--- wqflask/wqflask/search_results.py | 5 ++--- 5 files changed, 12 insertions(+), 16 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7ec764d8..c9dfe780 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -13,6 +13,7 @@ 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 wqflask import app @@ -25,8 +26,6 @@ from flask import Flask, g, request, url_for from utility.logger import getLogger logger = getLogger(__name__ ) -from wqflask import user_manager - class GeneralTrait(object): """ Trait class defines a trait in webqtl, can be either Microarray, @@ -304,7 +303,7 @@ def jsonable_table_row(trait, dataset_name, index): additive = "N/A" else: additive = "%.3f" % round(float(trait.additive), 2) - return ['', + return ['', index, ''+str(trait.name)+'', trait.symbol, @@ -320,7 +319,7 @@ def jsonable_table_row(trait, dataset_name, index): else: additive = "%.2f" % round(float(trait.additive), 2) if trait.pubmed_id: - return ['', + return ['', index, ''+str(trait.name)+'', trait.description_display, @@ -330,7 +329,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] else: - return ['', + return ['', index, ''+str(trait.name)+'', trait.description_display, @@ -340,7 +339,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] elif dataset.type == "Geno": - return ['', + return ['', index, ''+str(trait.name)+'', trait.location_repr] diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 0654e5d3..cc74c8e4 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -49,14 +49,13 @@ from utility.THCell import THCell from utility.TDCell import TDCell from base.trait import GeneralTrait from base import data_set -from utility import webqtlUtil, helper_functions, corr_result_helpers +from utility import webqtlUtil, helper_functions, corr_result_helpers, hmac from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string -from wqflask import user_manager from MySQLdb import escape_string as escape @@ -499,7 +498,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap for i, trait in enumerate(corr_results): results_dict = {} if not for_api: - results_dict['checkbox'] = "" + results_dict['checkbox'] = "" results_dict['index'] = i + 1 results_dict['trait_id'] = ""+str(trait.name)+"" else: diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 9c31bcfe..b5c45d05 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -46,7 +46,6 @@ import reaper import redis Redis = redis.StrictRedis() -from wqflask.user_manager import data_hmac from utility.THCell import THCell from utility.TDCell import TDCell from base.trait import GeneralTrait diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index b3a45f45..ed3b74b8 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -9,7 +9,7 @@ from db import webqtlDatabaseFunction from base import webqtlConfig -from wqflask import user_manager +from utility import hmac from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.benchmark import Bench @@ -70,7 +70,7 @@ class GSearch(object): this_trait['name'] = line[5] this_trait['dataset'] = line[3] this_trait['dataset_fullname'] = line[4] - this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[5], line[3])) + this_trait['hmac'] = hmac.hmac_creation('{}:{}'.format(line[5], line[3])) this_trait['species'] = line[0] this_trait['group'] = line[1] this_trait['tissue'] = line[2] @@ -174,7 +174,7 @@ class GSearch(object): this_trait['display_name'] = this_trait['name'] this_trait['dataset'] = line[2] this_trait['dataset_fullname'] = line[3] - this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[4], line[2])) + this_trait['hmac'] = hmac.hmac_creation('{}:{}'.format(line[4], line[2])) this_trait['species'] = line[0] this_trait['group'] = line[1] if line[9] != None and line[6] != None: diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index d76add67..902317a4 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -24,11 +24,10 @@ from wqflask import do_search from utility import webqtlUtil,tools from db import webqtlDatabaseFunction -from wqflask import user_manager - from flask import render_template, Flask, g from utility import formatting +from utility import hmac from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.logger import getLogger @@ -121,7 +120,7 @@ views.py). else: trait_dict['display_name'] = this_trait.name trait_dict['dataset'] = this_trait.dataset.name - trait_dict['hmac'] = user_manager.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) + trait_dict['hmac'] = hmac.hmac_creation('{}:{}'.format(this_trait.name, this_trait.dataset.name)) if this_trait.dataset.type == "ProbeSet": trait_dict['symbol'] = this_trait.symbol trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace') -- cgit v1.2.3