use _Sidebar order for nsgportal

Author: dungscout96

code/plugins/reformat_plugin.py

@@ -3,20 +3,36 @@
 import shutil
 
 # open a text file ending with .md and append a paragraph to it
-def reformat_wiki_pages(filepath, filename, parent, output_file):
-    with open(filepath) as f:
-        text = f.read()
-        append_text = '''---
+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)
+
+    if parent == "nsgportal":
+        pages = []
+        # 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 line.startswith('*'):
+                    # extract text between square brackets
+                    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)
+    
+    append_text += '---\n'
+
+    with open(filepath) as f:
+        text = f.read()
         text = append_text + text
-    with open(output_file, 'w') as out:
-        out.write(text)
+        with open(output_file, 'w') as out:
+            out.write(text)
 
 def reformat_plugin_dir(plugin_input_dir, plugin_name, order, plugin_type='wiki'):
     # plugins_output_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins'
@@ -70,7 +86,7 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, order, plugin_type='wiki'
         for root, dirs, files in os.walk(wiki_plugin_input_dir):
             for file in files:
                 if file.endswith('.md') and not file.startswith('index') and not file.startswith('Home'):
-                    reformat_wiki_pages(os.path.join(wiki_plugin_input_dir, file), file.strip('.md'), plugin_name, os.path.join(plugin_output_dir, file))
+                    reformat_wiki_pages(os.path.join(wiki_plugin_input_dir, file), file.strip('.md'), plugin_name, os.path.join(plugin_output_dir, file), wiki_plugin_input_dir)
 # main
 def main():
     if len(sys.argv) != 5:

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

@@ -4,6 +4,7 @@ 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
+nav_order: 8
 ---
 # Creating and managing a job from pop_nsg GUI
 In this tutorial we will address the creation and managing of NSG jobs from EEGLAB by using the plugin *nsgportal*. Specifically, the tutorial will focus on performing these tasks from the pop_nsg GUI.

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

@@ -4,6 +4,7 @@ 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
+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-plug-ins-on-NSG.md

@@ -4,6 +4,7 @@ title: EEGLAB-plug-ins-on-NSG
 long_title: EEGLAB-plug-ins-on-NSG
 parent: nsgportal
 grand_parent: Plugins
+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/Registering-at-NSG.md

@@ -4,6 +4,7 @@ title: Registering-at-NSG
 long_title: Registering-at-NSG
 parent: nsgportal
 grand_parent: Plugins
+nav_order: 1
 ---
 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).
 

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

@@ -4,5 +4,6 @@ title: Running-AMICA-on-NSG
 long_title: Running-AMICA-on-NSG
 parent: nsgportal
 grand_parent: Plugins
+nav_order: 11
 ---
 See this [page](https://github.com/japalmer29/amica/wiki/AMICA#how-to-run-amica-option-2-neuroscience-gateway-nsg) on the AMICA Gihub page.

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

@@ -4,6 +4,7 @@ title: Setting-up-the-plug-in
 long_title: Setting-up-the-plug-in
 parent: nsgportal
 grand_parent: Plugins
+nav_order: 4
 ---
 # Setting up the plug-in
 

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

@@ -4,6 +4,7 @@ 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
+nav_order: 10
 ---
 # Using pop_nsg command line tools in your EEGLAB plug-in
 

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

@@ -4,6 +4,7 @@ title: Using-the-Open-EEGLAB-Portal
 long_title: Using-the-Open-EEGLAB-Portal
 parent: nsgportal
 grand_parent: Plugins
+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/_Sidebar.md

@@ -9,12 +9,12 @@ grand_parent: Plugins
 * [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-ins on NSG](EEGLAB-plug-ins-on-NSG)
 # EEGLAB plug in to NSG: nsportal
 * [Setting up the plug-in](Setting-up-the-plug-in)
-* [Nsgportal plug-in GUI](https://github.com/sccn/nsgportal/wiki/nsgportal-graphical-user-interface:-pop_nsg)
+* [Nsgportal plug-in GUI](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)
+* [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)

plugins/nsgportal/index.md

@@ -4,7 +4,7 @@ title: nsgportal
 long_title: nsgportal
 parent: Plugins
 has_children: true
-nav_order: 5
+nav_order: 27
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/nsgportal).
 

plugins/nsgportal/nsgportal-command-line-tools.md

@@ -4,6 +4,7 @@ title: nsgportal-command-line-tools
 long_title: nsgportal-command-line-tools
 parent: nsgportal
 grand_parent: Plugins
+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/nsgportal-graphical-user-interface:-pop_nsg.md

@@ -4,6 +4,7 @@ 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