Fix root YAML variable in bin/lesson_initialize.py

[rnaseq-cwl-training.git] / bin / lesson_initialize.py

diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py
index 540bb08c83724f964570874b1b6e796640ac99d9..3ee1ace61cec7a8482dd439a59572bf579c48472 100755 (executable)
--- a/bin/lesson_initialize.py
+++ b/bin/lesson_initialize.py
@@ -45,7 +45,7 @@ This is a good way to introduce yourself
 and to meet some of our community members.
 
 1.  If you do not have a [GitHub][github] account,
 and to meet some of our community members.
 
 1.  If you do not have a [GitHub][github] account,

-    you can [send us comments by email][contact].
+    you can [send us comments by email][email].

     However,
     we will be able to respond more quickly if you use one of the other methods described below.
 
     However,
     we will be able to respond more quickly if you use one of the other methods described below.
 


@@ -151,9 +151,9 @@ and have final say over what gets merged into the lesson.
 General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
 happens on the [discussion mailing list][discuss-list],
 which everyone is welcome to join.
 General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
 happens on the [discussion mailing list][discuss-list],
 which everyone is welcome to join.

-You can also [reach us by email][contact].
+You can also [reach us by email][email].

 
 

-[contact]: mailto:admin@software-carpentry.org
+[email]: mailto:admin@software-carpentry.org

 [dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/
 [dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/


@@ -183,7 +183,7 @@ title: "Lesson Title"
 # Contact.  This *must* include the protocol: if it's an email
 # address, it must look like "mailto:lessons@software-carpentry.org",
 # or if it's a URL, "https://gitter.im/username/ProjectName".
 # Contact.  This *must* include the protocol: if it's an email
 # address, it must look like "mailto:lessons@software-carpentry.org",
 # or if it's a URL, "https://gitter.im/username/ProjectName".

-contact: "mailto:lessons@software-carpentry.org"
+email: "mailto:lessons@software-carpentry.org"

 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).


@@ -222,9 +222,10 @@ start_time: 0
 collections:
   episodes:
     output: true
 collections:
   episodes:
     output: true

-    permalink: /:path/
+    permalink: /:path/index.html

   extras:
     output: true
   extras:
     output: true

+    permalink: /:path/index.html

 
 # Set the default layout for things in the episodes collection.
 defaults:
 
 # Set the default layout for things in the episodes collection.
 defaults:


@@ -249,6 +250,7 @@ ROOT_INDEX_MD = '''\
 ---
 layout: lesson
 root: .
 ---
 layout: lesson
 root: .

+permalink: index.html  # Is the only page that don't follow the partner /:path/index.html

 ---
 FIXME: home page introduction
 
 ---
 FIXME: home page introduction
 


@@ -261,7 +263,7 @@ FIXME: home page introduction
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference

-permalink: /reference/
+root: .

 ---
 
 ## Glossary
 ---
 
 ## Glossary


@@ -273,11 +275,50 @@ ROOT_SETUP_MD = '''\
 ---
 layout: page
 title: Setup
 ---
 layout: page
 title: Setup

-permalink: /setup/
+root: .

 ---
 FIXME
 '''
 
 ---
 FIXME
 '''
 

+ROOT_AIO_MD = '''\
+---
+layout: page 
+root: .
+---
+<script>
+  window.onload = function() {
+    var lesson_episodes = [
+    {% for episode in site.episodes %}
+    "{{ episode.url}}"{% unless forloop.last %},{% endunless %}
+    {% endfor %}
+    ];
+    var xmlHttp = [];  /* Required since we are going to query every episode. */
+    for (i=0; i < lesson_episodes.length; i++) {
+      xmlHttp[i] = new XMLHttpRequest();
+      xmlHttp[i].episode = lesson_episodes[i];  /* To enable use this later. */
+      xmlHttp[i].onreadystatechange = function() {
+      if (this.readyState == 4 && this.status == 200) {
+        var article_here = document.getElementById(this.episode);
+        var parser = new DOMParser();
+        var htmlDoc = parser.parseFromString(this.responseText,"text/html");
+        var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
+        article_here.innerHTML = htmlDocArticle.innerHTML;
+        }
+      }
+      episode_url = "{{ page.root }}" + lesson_episodes[i];
+      xmlHttp[i].open("GET", episode_url);
+      xmlHttp[i].send(null);
+    }
+  }
+</script>
+{% comment %}
+Create anchor for each one of the episodes.
+{% endcomment %}
+{% for episode in site.episodes %}
+<article id="{{ episode.url }}"></article>
+{% endfor %}
+'''
+

 EPISODES_INTRODUCTION_MD = '''\
 ---
 title: "Introduction"
 EPISODES_INTRODUCTION_MD = '''\
 ---
 title: "Introduction"


@@ -296,7 +337,6 @@ EXTRAS_ABOUT_MD = '''\
 ---
 layout: page
 title: About
 ---
 layout: page
 title: About

-permalink: /about/

 ---
 {% include carpentries.html %}
 '''
 ---
 {% include carpentries.html %}
 '''


@@ -305,7 +345,6 @@ EXTRAS_DISCUSS_MD = '''\
 ---
 layout: page
 title: Discussion
 ---
 layout: page
 title: Discussion

-permalink: /discuss/

 ---
 FIXME
 '''
 ---
 FIXME
 '''


@@ -314,24 +353,52 @@ EXTRAS_FIGURES_MD = '''\
 ---
 layout: page
 title: Figures
 ---
 layout: page
 title: Figures

-permalink: /figures/

 ---
 ---

-{% include all_figures.html %}
+<script>
+  window.onload = function() {
+    var lesson_episodes = [
+    {% for episode in site.episodes %}
+    "{{ episode.url}}"{% unless forloop.last %},{% endunless %}
+    {% endfor %}
+    ];
+    var xmlHttp = [];  /* Required since we are going to query every episode. */
+    for (i=0; i < lesson_episodes.length; i++) {
+      xmlHttp[i] = new XMLHttpRequest();
+      xmlHttp[i].episode = lesson_episodes[i];  /* To enable use this later. */
+      xmlHttp[i].onreadystatechange = function() {
+        if (this.readyState == 4 && this.status == 200) {
+          var article_here = document.getElementById(this.episode);
+          var parser = new DOMParser();
+          var htmlDoc = parser.parseFromString(this.responseText,"text/html");
+          var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
+          article_here.appendChild(htmlDocArticle.getElementsByTagName("h1")[0]);
+          for (let image of htmlDocArticle.getElementsByTagName("img")) {
+            article_here.appendChild(image);
+          }
+        }
+      }
+      episode_url = "{{ page.root }}" + lesson_episodes[i];
+      xmlHttp[i].open("GET", episode_url);
+      xmlHttp[i].send(null);
+    }
+  }
+</script>
+{% comment %}
+Create anchor for each one of the episodes.
+{% endcomment %}
+{% for episode in site.episodes %}
+<article id="{{ episode.url }}"></article>
+{% endfor %}

 '''
 
 EXTRAS_GUIDE_MD = '''\
 ---
 layout: page
 title: "Instructor Notes"
 '''
 
 EXTRAS_GUIDE_MD = '''\
 ---
 layout: page
 title: "Instructor Notes"

-permalink: /guide/

 ---
 FIXME
 '''
 
 ---
 FIXME
 '''
 

-INCLUDES_ALL_FIGURES_HTML = '''\
-<!-- empty -->
-'''
-

 BOILERPLATE = (
     ('AUTHORS', ROOT_AUTHORS),
     ('CITATION', ROOT_CITATION),
 BOILERPLATE = (
     ('AUTHORS', ROOT_AUTHORS),
     ('CITATION', ROOT_CITATION),


@@ -340,12 +407,12 @@ BOILERPLATE = (
     ('index.md', ROOT_INDEX_MD),
     ('reference.md', ROOT_REFERENCE_MD),
     ('setup.md', ROOT_SETUP_MD),
     ('index.md', ROOT_INDEX_MD),
     ('reference.md', ROOT_REFERENCE_MD),
     ('setup.md', ROOT_SETUP_MD),

+    ('aio.md', ROOT_AIO_MD),

     ('_episodes/01-introduction.md', EPISODES_INTRODUCTION_MD),
     ('_extras/about.md', EXTRAS_ABOUT_MD),
     ('_extras/discuss.md', EXTRAS_DISCUSS_MD),
     ('_extras/figures.md', EXTRAS_FIGURES_MD),
     ('_extras/guide.md', EXTRAS_GUIDE_MD),
     ('_episodes/01-introduction.md', EPISODES_INTRODUCTION_MD),
     ('_extras/about.md', EXTRAS_ABOUT_MD),
     ('_extras/discuss.md', EXTRAS_DISCUSS_MD),
     ('_extras/figures.md', EXTRAS_FIGURES_MD),
     ('_extras/guide.md', EXTRAS_GUIDE_MD),

-    ('_includes/all_figures.html', INCLUDES_ALL_FIGURES_HTML)

 )
 
 
 )