From be09d207ee4e2705e358102f8bdbcd1da7f70ca2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 24 Apr 2020 16:06:36 -0500 Subject: Replaced hard-coded instances of GN2 urls with ones pulled from settings file --- wqflask/base/data_set.py | 4 ++-- wqflask/base/trait.py | 7 ++++--- wqflask/utility/tools.py | 2 ++ wqflask/wqflask/ctl/ctl_analysis.py | 4 +++- wqflask/wqflask/do_search.py | 3 ++- wqflask/wqflask/network_graph/network_graph.py | 2 ++ wqflask/wqflask/search_results.py | 3 ++- wqflask/wqflask/static/new/javascript/ctl_graph.js | 8 +------- wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js | 1 - wqflask/wqflask/static/new/javascript/network_graph.js | 4 ++-- wqflask/wqflask/templates/ctl_results.html | 1 + wqflask/wqflask/templates/index_page.html | 4 ++-- wqflask/wqflask/templates/index_page_orig.html | 4 ++-- wqflask/wqflask/templates/network_graph.html | 1 + 14 files changed, 26 insertions(+), 22 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fae62875..8652e6b7 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -56,7 +56,7 @@ from pprint import pformat as pf from db.gn_server import menu_main from db.call import fetchall,fetchone,fetch1 -from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL from utility.logger import getLogger logger = getLogger(__name__ ) @@ -94,7 +94,7 @@ Publish or ProbeSet. E.g. """ self.datasets = {} if rebuild: #ZS: May make this the only option - data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content) + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) #data = gen_menu.gen_dropdown_json() else: file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 5525472e..e454c593 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -14,6 +14,7 @@ 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 wqflask import app @@ -135,9 +136,9 @@ 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) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 0fbedccb..9354ece6 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -234,6 +234,8 @@ def show_settings(): GN_VERSION = get_setting('GN_VERSION') HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') +GN2_BASE_URL = get_setting('GN2_BASE_URL') +GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') GN_SERVER_URL = get_setting('GN_SERVER_URL') SERVER_PORT = get_setting_int('SERVER_PORT') SQL_URI = get_setting('SQL_URI') diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 6fda02fd..4415b86a 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -20,7 +20,7 @@ from base import data_set from base import trait as TRAIT from utility import helper_functions -from utility.tools import locate +from utility.tools import locate, GN2_BRANCH_URL from rpy2.robjects.packages import importr @@ -56,6 +56,8 @@ class CTL(object): self.edges_list = [] logger.info("Obtained pointers to CTL functions") + self.gn2_url = GN2_BRANCH_URL + def addNode(self, gt): node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name), 'sid' : str(gt.name), diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 05caa100..b0ca5ced 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -13,6 +13,7 @@ import sys # sys.path.append("..") Never in a running webserver from db import webqtlDatabaseFunction +from utility.tools import GN2_BASE_URL import logging from utility.logger import getLogger @@ -919,7 +920,7 @@ def get_aliases(symbol, species): return [] filtered_aliases = [] - response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + symbol_string) + response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) if response: alias_list = json.loads(response.content) diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index a332db46..152e4168 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -47,6 +47,7 @@ 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.tools import GN2_BRANCH_URL from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions @@ -195,6 +196,7 @@ class NetworkGraph(object): self.nodes_list.append(node_dict) self.elements = json.dumps(self.nodes_list + self.edges_list) + self.gn2_url = GN2_BRANCH_URL groups = [] for sample in self.all_sample_list: diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 698389ab..8f702d58 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -28,6 +28,7 @@ from flask import render_template, Flask, g from utility import formatting from utility import hmac +from utility.tools import GN2_BASE_URL from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.logger import getLogger @@ -295,7 +296,7 @@ def get_aliases(symbol_list, species): symbols_string = ",".join(updated_symbols) filtered_aliases = [] - response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases2/" + symbols_string) + response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string) if response: alias_lists = json.loads(response.content) seen = set() diff --git a/wqflask/wqflask/static/new/javascript/ctl_graph.js b/wqflask/wqflask/static/new/javascript/ctl_graph.js index 94bd7e9d..bd950592 100644 --- a/wqflask/wqflask/static/new/javascript/ctl_graph.js +++ b/wqflask/wqflask/static/new/javascript/ctl_graph.js @@ -82,18 +82,12 @@ window.onload=function() { function create_qtips(cy){ cy.nodes().qtip({ content: function(){ - gn_link = ''+''+this.data().id +''+'
' + gn_link = ''+''+this.data().id +''+'
' ncbi_link = 'NCBI'+'
' omim_link = 'OMIM'+'
' qtip_content = gn_link + ncbi_link + omim_link return qtip_content - //return ''+''+this.data().id +''+'' }, - // content: { - // title: ''+''+this.target() +''+'', - // text: this.target, - // button: true - // }, position: { my: 'top center', at: 'bottom center' diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index fad600d2..794804f4 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -74,7 +74,6 @@ redo_dropdown = function(dropdown, items) { this_opt_group = null for (_i = 0, _len = group_family_list.length; _i < _len; _i++) { item = group_family_list[_i]; - console.log("THE ITEM:", item) if (item[2] != "None" && current_family == ""){ current_family = item[2] this_opt_group = $("") diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js index 4d507a18..02c3b817 100644 --- a/wqflask/wqflask/static/new/javascript/network_graph.js +++ b/wqflask/wqflask/static/new/javascript/network_graph.js @@ -85,7 +85,7 @@ window.onload=function() { cy.nodes().qtip({ content: function(){ qtip_content = '' - gn_link = ''+''+this.data().id +''+'
' + gn_link = ''+''+this.data().id +''+'
' qtip_content += gn_link if (typeof(this.data().geneid) !== 'undefined'){ ncbi_link = 'NCBI'+'
' @@ -115,7 +115,7 @@ window.onload=function() { correlation_line = 'Sample r: ' + this.data().correlation + '
' p_value_line = 'Sample p(r): ' + this.data().p_value + '
' overlap_line = 'Overlap: ' + this.data().overlap + '
' - scatter_plot = 'View Scatterplot' + scatter_plot = 'View Scatterplot' return correlation_line + p_value_line + overlap_line + scatter_plot }, position: { diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html index d85075a9..0108d93a 100644 --- a/wqflask/wqflask/templates/ctl_results.html +++ b/wqflask/wqflask/templates/ctl_results.html @@ -61,6 +61,7 @@ diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 0116245d..f8720d39 100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -219,9 +219,9 @@

GN1 Mirror and development sites

diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 963531cb..06b71f53 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -254,8 +254,8 @@

GeneNetwork v2:

GeneNetwork v1: