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)