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

plugins/nsgportal/Running-AMICA-on-NSG.md

@@ -1,9 +1,10 @@
 ---
 layout: default
-title: Using-pop_nsg-command-line-tools-in-your-EEGLAB-plug-in
-long_title: Using-pop_nsg-command-line-tools-in-your-EEGLAB-plug-in
 parent: nsgportal
 grand_parent: Plugins
+
+title: Tutorial 3-Using in other EEGLAB plug-ins
+long_title: Tutorial 3-Using in other EEGLAB plug-ins
 nav_order: 10
 ---
 # Using pop_nsg command line tools in your EEGLAB plug-in

plugins/nsgportal/Scheme-of-plug-in-functions-call.md

@@ -1,9 +1,10 @@
 ---
 layout: default
-title: Using-the-Open-EEGLAB-Portal
-long_title: Using-the-Open-EEGLAB-Portal
 parent: nsgportal
 grand_parent: Plugins
+
+title: Using the Open EEGLAB Portal
+long_title: Using the Open EEGLAB Portal
 nav_order: 2
 ---
 There will be two approaches to using the Open EEGLAB Portal: either, through its NSG web interface (http://www.NSGportal.org), or by making use of the NSG command line RESTful interface (NSG-R). This section describes the use of the web interface.

plugins/nsgportal/Setting-up-the-plug-in.md

@@ -1,22 +1,18 @@
 ---
 layout: default
-title: _Sidebar
-long_title: _Sidebar
 parent: nsgportal
 grand_parent: Plugins
 ---
 # EEGLAB on NSG
-* [EEGLAB on NSG](Home)
 * [Registering on NSG](Registering-at-NSG)
 * [Using the Open EEGLAB Portal](Using-the-Open-EEGLAB-Portal)
 * [EEGLAB plug-ins on NSG](EEGLAB-plug-ins-on-NSG)
-# EEGLAB plug in to NSG: nsportal
+# EEGLAB plug in to NSG
 * [Setting up the plug-in](Setting-up-the-plug-in)
-* [Nsgportal plug-in GUI](nsgportal-graphical-user-interface:-pop_nsg)
+* [Nsgportal plug-in GUI](https://github.com/sccn/nsgportal/wiki/nsgportal-graphical-user-interface:-pop_nsg)
 * [Nsgportal command line tools](nsgportal-command-line-tools)
 * [Scheme of plug-in functions call](scheme-of-plug-in-functions-call)
 # Tutorials
-* [Tutorial 1: Creating and managing an NSG job from the _pop_nsg_ GUI](Creating-and-managing-a-job-from-pop_nsg-GUI)
-* [Tutorial 2: Creating and managing an NSG job using _pop_nsg_ from the command line](Creating-and-managing-an-NSG-job-using-pop_nsg-from-the-command-line)
-* [Tutorial 3: Using _pop_nsg_ in an EEGLAB plug-in](Using-pop_nsg-command-line-tools-in-your-EEGLAB-plug-in)
-* [Tutorial 4: Running AMICA on NSG](Running-AMICA-on-NSG)
+* [Tutorial 1-GUI job management](Creating-and-managing-a-job-from-pop_nsg-GUI)
+* [Tutorial 2-Command line management](Creating-and-managing-an-NSG-job-using-pop_nsg-from-the-command-line)
+* [Tutorial 3-Using in other EEGLAB plug-ins](Using-pop_nsg-command-line-tools-in-your-EEGLAB-plug-in)

plugins/nsgportal/Using-pop_nsg-command-line-tools-in-your-EEGLAB-plug-in.md

@@ -1,9 +1,10 @@
 ---
 layout: default
-title: nsgportal-command-line-tools
-long_title: nsgportal-command-line-tools
 parent: nsgportal
 grand_parent: Plugins
+
+title: Nsgportal command line tools
+long_title: Nsgportal command line tools
 nav_order: 6
 ---
 Just like many other EEGLAB functions, users can interact with *nsgportal* through either the graphic user interface or using command line tools. The command line tools allow users to largely automate their analysis and make the process easy to reproduce. In this section, we introduce the *nsgportal* command line tools to NSG.

plugins/nsgportal/Using-the-Open-EEGLAB-Portal.md

@@ -1,10 +1,7 @@
 ---
 layout: default
-title: nsgportal-graphical-user-interface:-pop_nsg
-long_title: nsgportal-graphical-user-interface:-pop_nsg
 parent: nsgportal
 grand_parent: Plugins
-nav_order: 5
 ---
 
 # *nsgportal* graphical user interface: pop_nsg