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,
-    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.
 
@@ -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.
-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/
@@ -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: "mailto:lessons@software-carpentry.org"
+email: "mailto:lessons@software-carpentry.org"
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
@@ -222,9 +222,10 @@ start_time: 0
 collections:
   episodes:
     output: true
-    permalink: /:path/
+    permalink: /:path/index.html
   extras:
     output: true
+    permalink: /:path/index.html
 
 # Set the default layout for things in the episodes collection.
 defaults:
@@ -249,6 +250,7 @@ ROOT_INDEX_MD = '''\
 ---
 layout: lesson
 root: .
+permalink: index.html  # Is the only page that don't follow the partner /:path/index.html
 ---
 FIXME: home page introduction
 
@@ -261,7 +263,7 @@ FIXME: home page introduction
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference
-permalink: /reference/
+root: .
 ---
 
 ## Glossary
@@ -273,11 +275,50 @@ ROOT_SETUP_MD = '''\
 ---
 layout: page
 title: Setup
-permalink: /setup/
+root: .
 ---
 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"
@@ -296,7 +337,6 @@ EXTRAS_ABOUT_MD = '''\
 ---
 layout: page
 title: About
-permalink: /about/
 ---
 {% include carpentries.html %}
 '''
@@ -305,7 +345,6 @@ EXTRAS_DISCUSS_MD = '''\
 ---
 layout: page
 title: Discussion
-permalink: /discuss/
 ---
 FIXME
 '''
@@ -314,24 +353,52 @@ EXTRAS_FIGURES_MD = '''\
 ---
 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"
-permalink: /guide/
 ---
 FIXME
 '''
 
-INCLUDES_ALL_FIGURES_HTML = '''\
-<!-- empty -->
-'''
-
 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),
+    ('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),
-    ('_includes/all_figures.html', INCLUDES_ALL_FIGURES_HTML)
 )