Feature/fix wgcna api path (#630)

* add correct path gn3 api endpoint

* remove ununsed dependencies;replace libraries with ones from guix

* replace xterm cdn libs

2 files changed, 12 insertions, 35 deletions

diff --git a/wqflask/wqflask/templates/wgcna_setup.html b/wqflask/wqflask/templates/wgcna_setup.html
index 86d9fa10..d7acd5f2 100644
--- a/wqflask/wqflask/templates/wgcna_setup.html
+++ b/wqflask/wqflask/templates/wgcna_setup.html
@@ -9,7 +9,8 @@
 }
 
 </style>
-<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/xterm@4.14.1/css/xterm.css">
+
+<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='xterm/xterm.min.css') }}" />
 
 <div class="container">
     <div class="col-md-5">
@@ -80,19 +81,12 @@
 </div>
 </div>
 
-<script src="https://cdn.socket.io/4.2.0/socket.io.min.js" integrity="sha384-PiBR5S00EtOj2Lto9Uu81cmoyZqR57XcOna1oAuVuIEjzj0wpqDVfD0JA9eXlRsj" crossorigin="anonymous"></script>
-
-<script src="https://cdn.jsdelivr.net/npm/xterm@4.14.1/lib/xterm.min.js"></script>
-
-<script src="https://cdn.jsdelivr.net/npm/xterm-addon-attach@0.6.0/lib/xterm-addon-attach.min.js"></script>
-
-
+<script src="{{ url_for('js', filename='xterm/xterm.min.js') }}" type="text/javascript"></script>
+<script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
 <script src="https://cdn.jsdelivr.net/npm/xterm-addon-fit@0.5.0/lib/xterm-addon-fit.min.js"></script>
- <script src="https://code.jquery.com/jquery-3.5.1.js"
-          integrity="sha256-QWo7LDvxbWT2tbbQ97B53yJnYU3WhH/C8ycbRAkjPDc="
-          crossorigin="anonymous"></script>
+
 <script>
-// document.addEventListener('DOMContentLoaded', function() {
+document.addEventListener('DOMContentLoaded', function() {
 let term = new Terminal({
     cursorBlink: true,
     lineHeight: 1.3,
@@ -117,11 +111,6 @@ term.writeln(termDebugs.general)
 
 wgcnaForm = document.querySelector("#wgcna_form")
 
-const socket = io("http://127.0.0.1:8081") //issue gn3 private
-const attachAddon = new AttachAddon.AttachAddon(socket);
-
-term.loadAddon(attachAddon);
-
 fitAddon.fit()
 term.onData((data) => {
     term.write(data)
@@ -133,16 +122,6 @@ if (wgcnaForm) {
     term.writeln(termDebugs.fail)
 }
 
-socket.on("connect", () => {
-    $("#wgcna_form").append(`<input type="hidden" name="socket_id" value=${socket.id}>`);
-})
-
-socket.on("output", ({
-    data
-}) => {
-    term.writeln(data)
-})
-
 $(document).on('submit', '#wgcna_form', function(e) {
     term.writeln(termDebugs.success)
 
@@ -156,6 +135,8 @@ $(document).on('submit', '#wgcna_form', function(e) {
             document.write(data)
         }
     })
-});
+})
+})
+
 </script>
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/wgcna/gn3_wgcna.py b/wqflask/wqflask/wgcna/gn3_wgcna.py
index c4cc2e7f..15728f22 100644
--- a/wqflask/wqflask/wgcna/gn3_wgcna.py
+++ b/wqflask/wqflask/wgcna/gn3_wgcna.py
@@ -4,7 +4,9 @@ and process data to be rendered by datatables
 
 import requests
 from types import SimpleNamespace
+
 from utility.helper_functions import get_trait_db_obs
+from utility.tools import GN_SERVER_URL
 
 
 def fetch_trait_data(requestform):
@@ -24,7 +26,6 @@ def process_dataset(trait_list):
     traits = []
     strains = []
 
-    # xtodo unique traits and strains
 
     for trait in trait_list:
         traits.append(trait[0].name)
@@ -33,9 +34,6 @@ def process_dataset(trait_list):
         for strain in trait[0].data:
             strains.append(strain)
             input_data[trait[0].name][strain] = trait[0].data[strain].value
-        # "sample_names": list(set(strains)),
-        # "trait_names": form_traits,
-        # "trait_sample_data": form_strains,
 
     return {
         "input": input_data,
@@ -77,9 +75,7 @@ def process_image(response):
 def run_wgcna(form_data):
     """function to run wgcna"""
 
-    GN3_URL = "http://127.0.0.1:8081"
-
-    wgcna_api = f"{GN3_URL}/api/wgcna/run_wgcna"
+    wgcna_api = f"{GN_SERVER_URL}api/wgcna/run_wgcna"
 
     # parse form data