update nsgportal and sidebar mechanism

Author: dungscout96

code/plugins/reformat_plugin.py

@@ -6,26 +6,39 @@
 def reformat_wiki_pages(filepath, filename, parent, output_file, wiki_input_dir=""):
     append_text = '''---
 layout: default
-title: {filename}
-long_title: {filename}
 parent: {parent}
 grand_parent: Plugins
 '''.format(filename=filename, parent=parent)
 
-    print(f"Reformatting {filename}...")
+    print(f"Reformatting {filename} of {parent}...")
     if parent in ["nsgportal", "limo"]:
         pages = []
+        titles = []
         # load _Sidebar.md and extract all links from markdown file
         with open(os.path.join(wiki_input_dir, '_Sidebar.md')) as f:
             lines = f.readlines()
             for line in lines:
                 if '(' in line:
                     # extract text between square brackets
+                    title = line[line.find('[')+1:line.find(']')]
                     page = line[line.find('(')+1:line.find(')')]
                     pages.append(page)
-        if filename in pages:
-            order = pages.index(filename)
-            append_text += 'nav_order: {order}\n'.format(order=order)
+                    titles.append(title)
+        pages = list(map(str.lower, pages))
+        if filename.lower() in pages:
+            order = pages.index(filename.lower())
+            title = titles[order]
+            append_text += '''
+title: {title}
+long_title: {title}
+'''.format(title=title)
+
+            append_text += 'nav_order: {order}\n'.format(order=order+1)
+    else:   
+        append_text += '''
+title: {filename}
+long_title: {filename}
+'''.format(filename=filename)
 
     append_text += '---\n'
 

plugins/nsgportal/Creating-and-managing-a-job-from-pop_nsg-GUI.md

@@ -1,9 +1,10 @@
 ---
 layout: default
-title: Creating-and-managing-a-job-from-pop_nsg-GUI
-long_title: Creating-and-managing-a-job-from-pop_nsg-GUI
 parent: nsgportal
 grand_parent: Plugins
+
+title: Tutorial 1-GUI job management
+long_title: Tutorial 1-GUI job management
 nav_order: 8
 ---
 # Creating and managing a job from pop_nsg GUI

plugins/nsgportal/Creating-and-managing-an-NSG-job-using-pop_nsg-from-the-command-line.md

@@ -1,9 +1,10 @@
 ---
 layout: default
-title: Creating-and-managing-an-NSG-job-using-pop_nsg-from-the-command-line
-long_title: Creating-and-managing-an-NSG-job-using-pop_nsg-from-the-command-line
 parent: nsgportal
 grand_parent: Plugins
+
+title: Tutorial 2-Command line management
+long_title: Tutorial 2-Command line management
 nav_order: 9
 ---
 This tutorial describes in details the process of submitting and managing a job using the command line options in _pop_nsg_. 

plugins/nsgportal/EEGLAB-command-line-tools-to-RESTful-interface.md

@@ -1,9 +1,10 @@
 ---
 layout: default
-title: EEGLAB-plug-ins-on-NSG
-long_title: EEGLAB-plug-ins-on-NSG
 parent: nsgportal
 grand_parent: Plugins
+
+title: EEGLAB plug-ins on NSG
+long_title: EEGLAB plug-ins on NSG
 nav_order: 3
 ---
 The EEGLAB installation on NSG provides access to most of the EEGLAB plug-ins. See the table below for the list below of plug-in available from EEGLAB at NSG, as well as important links to the use of these plugins

plugins/nsgportal/EEGLAB-plug-ins-on-NSG.md

@@ -1,11 +1,14 @@
 ---
 layout: default
-title: Registering-at-NSG
-long_title: Registering-at-NSG
 parent: nsgportal
 grand_parent: Plugins
+
+title: Registering on NSG
+long_title: Registering on NSG
 nav_order: 1
 ---
+There are two ways to access to NSG: via NSG portal and through the command line interface NSG-R. The latter one uses its core curl commands to communicate with NSG and is the interface used by the nsgportal plug-in. Since both ways are interfaces to NSG, If you have already registered to NSG, you can use the same login and password for NSG-R. For the REST interface, refer to the [NSG REST documentation](https://nsgr.sdsc.edu:8443/restusers/documentation).
+
 The first step to using the Open EEGLAB Portal is to create an NSG account [HERE](https://www.nsgportal.org/gest/reg.php) (or by clicking on "Register account" on the NSG home page).
 
 <center>

plugins/nsgportal/Registering-at-NSG.md

@@ -1,9 +1,11 @@
 ---
 layout: default
-title: Scheme-of-plug-in-functions-call
-long_title: Scheme-of-plug-in-functions-call
 parent: nsgportal
 grand_parent: Plugins
+
+title: Scheme of plug-in functions call
+long_title: Scheme of plug-in functions call
+nav_order: 7
 ---
 The figure below shows a scheme of function calls in _nsgportal_. In the plug-in there are two main sets, or layers, of functions designated by the prefix _pop__ and _nsg__. The _pop__ functions open a parameter entry window when called with fewer than the required arguments, else run directly without opening a window.  The second class of nsgportal functions with prefix _nsg__ can be called directly from MATLAB command line or from other MATLAB scripts or functions. These functions perform lower-level processing than the pop_ functions. A plug-in function (_eegplugin_nsgportal_) manages the inclusion and appearance of an nsgportal item in the main EEGLAB window menu. 
 

plugins/nsgportal/Registering-on-NSG-R.md

@@ -1,9 +1,10 @@
 ---
 layout: default
-title: Setting-up-the-plug-in
-long_title: Setting-up-the-plug-in
 parent: nsgportal
 grand_parent: Plugins
+
+title: Setting up the plug-in
+long_title: Setting up the plug-in
 nav_order: 4
 ---
 # Setting up the plug-in