--- /dev/null
+Arvados Documentation
+
+0. Install dependencies
+
+ $ bundle install
+
+
+1. To build or update documentation:
+ $ rake generate
+
+
+2. To view documentation:
+ $ rake run
+[2014-03-10 09:03:41] INFO WEBrick 1.3.1
+[2014-03-10 09:03:41] INFO ruby 2.1.1 (2014-02-24) [x86_64-linux]
+[2014-03-10 09:03:41] INFO WEBrick::HTTPServer#start: pid=8926 port=8000
+
+ Then go to http://localhost:8000
+
+
+2. You can set 'baseurl' (the URL prefix for all internal links),
+'arvados_api_host' and 'arvados_workbench_host' without changing _config.yml:
+
+ $ rake generate baseurl=/example arvados_api_host=example.com
+
+
+4. To delete generated files:
+ $ rake realclean
require "rubygems"
require "colorize"
+task :generate do
+ vars = ['baseurl', 'arvados_api_host', 'arvados_workbench_host']
+ vars.each do |v|
+ if ENV[v]
+ website.config.h[v] = ENV[v]
+ end
+ end
+end
+
require "zenweb/tasks"
load "zenweb-textile.rb"
load "zenweb-liquid.rb"
# file:///tmp/arvados/doc/.site). To make docs show up inside
# workbench, use /doc here and add a symlink at
# apps/workbench/public/doc pointing to ../../../doc/.site
+# You can also set these on the command line:
+# $ rake generate baseurl=/example arvados_api_host=example.comA
-baseurl: /doc
+baseurl:
+arvados_api_host: localhost
+arvados_workbench_host: localhost
exclude: ["Rakefile", "tmp", "vendor"]
-arvados_api_host: qr1hi.arvadosapi.com
navbar:
userguide:
<link href="{{ site.baseurl }}/css/bootstrap.css" rel="stylesheet">
<link href="{{ site.baseurl }}/css/nav-list.css" rel="stylesheet">
<link href="{{ site.baseurl }}/css/badges.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/code.css" rel="stylesheet">
<style>
html {
height:100%;
text-align: center;
margin-bottom: 1em;
}
- .userinput {
- color: #d14;
- }
:target {
padding-top: 61px;
margin-top: -61px;
--- /dev/null
+table.code {
+ font-family: Menlo,Monaco,Consolas,"Courier New",monospace;
+ display: block;
+ padding: 9.5px;
+ margin: 0px 0px 10px;
+ font-size: 13px;
+ line-height: 1.42857;
+ color: rgb(51, 51, 51);
+ word-break: break-all;
+ word-wrap: break-word;
+ background-color: rgb(245, 245, 245);
+ border: 1px solid rgb(204, 204, 204);
+ border-radius: 4px 4px 4px 4px;
+}
+
+table.code tr td {
+ white-space: pre;
+}
+
+table.code tr td:nth-child(2) {
+ color: #d14;
+ padding-left: .5em;
+}
+
+.userinput {
+ color: #d14;
+}
</div>
<div class="col-sm-7" style="border-left: solid; border-width: 1px">
<p>
- <a href="{{ site.baseurl }}/user/">User Guide</a> — How to manage data and do analysis with Arvados.
+ <a href="{{ site.baseurl }}/user/index.html">User Guide</a> — How to manage data and do analysis with Arvados.
</p>
<p>
- <a href="{{ site.baseurl }}/sdk/">SDK Reference</a> — Details about the accessing Arvados from various programming languages.
+ <a href="{{ site.baseurl }}/sdk/index.html">SDK Reference</a> — Details about the accessing Arvados from various programming languages.
</p>
<p>
- <a href="{{ site.baseurl }}/api/">API Reference</a> — Details about the the Arvados REST API.
+ <a href="{{ site.baseurl }}/api/index.html">API Reference</a> — Details about the the Arvados REST API.
</p>
<p>
- <a href="{{ site.baseurl }}/admin/">Admin Guide</a> — How to administer an Arvados system.
+ <a href="{{ site.baseurl }}/admin/index.html">Admin Guide</a> — How to administer an Arvados system.
</p>
<p>
- <a href="{{ site.baseurl }}/install/">Install Guide</a> — How to install Arvados on a cloud platform.
+ <a href="{{ site.baseurl }}/install/index.html">Install Guide</a> — How to install Arvados on a cloud platform.
</p>
</div>
</div>
# Programming in @python@
# Revision control using @git@
-The examples in this guide uses the public Arvados instance located at "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ . You must have an account in order to use this service. If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com .
+The examples in this guide uses the Arvados instance located at "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/ . If you are using a different Arvados instance replace @{{ site.arvados_workbench_host }}@ with your private instance in all of the examples in this guide.
-If you are using a different Arvados instance replace @{{ site.arvados_api_host }}@ with your private instance in all of the examples in this guide.
+The Arvados public beta instance is located at "https://workbench.qr1hi.arvadosapi.com/":https://workbench.qr1hi.arvadosapi.com/ . You must have an account in order to use this service. If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com .
h2. Typographic conventions
<notextile>
<ul>
-<li>Code blocks which are set aside from the text indicate user input to the system. Commands that should be entered into a Unix shell are indicated by the directory where you should enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black. For example, the following block indicates that you should type "ls foo" while in your home directory and the expected output will be "foo".
-
+<li>Code blocks which are set aside from the text indicate user input to the system. Commands that should be entered into a Unix shell are indicated by the directory where you should enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black. For example, the following block indicates that you should type "ls foo.*" while in your home directory and the expected output will be "foo.input" and "foo.output".
<pre><code>~$ <span class="userinput">ls foo</span>
foo
-</code></pre></li>
+</code></pre>
+</li>
<li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
<li>Bold text emphasizes <b>specific items</b> to look when discussing Arvados Workbench pages.</li>
Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
-<pre><code class="userinput">{% include 'run_md5sum_py' %}</code></pre>
+<notextile> {% code 'run_md5sum_py' as python %} </notextile>
Make the file executable:
Add the following code to compute the md5 hash of each file in a collection:
-<pre><code class="userinput">{% include 'tutorial_hash_script_py' %}</code></pre>
+<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
Make the file executable:
Our second script will filter the output of @parallel_hash.py@ and only include hashes that start with 0. Create a new script in @crunch_scripts/@ called @0-filter.py@:
-<pre><code class="userinput">{% include '0_filter_py' %}</code></pre>
+<notextile> {% code '0_filter_py' as python %} </notextile>
Now add it to git:
Add the following code to compute the md5 hash of each file in a
-<pre><code class="userinput">{% include 'parallel_hash_script_py' %}</code></pre>
+<notextile> {% code 'parallel_hash_script_py' as python %} </notextile>
Make the file executable:
require 'zenweb'
+require 'liquid'
module ZenwebLiquid
VERSION = '0.0.1'
##
# Render a page's liquid and return the intermediate result
def liquid template, content, page, binding = TOPLEVEL_BINDING
- require 'liquid'
Liquid::Template.file_system = Liquid::LocalFileSystem.new(File.join(File.dirname(Rake.application().rakefile), "_includes"))
unless defined? @liquid_template
@liquid_template = Liquid::Template.parse(template)
@liquid_template.render(vars)
end
end
+
+ class LiquidCode < Liquid::Include
+ Syntax = /(#{Liquid::QuotedFragment}+)(\s+(?:as)\s+(#{Liquid::QuotedFragment}+))?/o
+
+ def initialize(tag_name, markup, tokens)
+ Liquid::Tag.instance_method(:initialize).bind(self).call(tag_name, markup, tokens)
+
+ if markup =~ Syntax
+ @template_name = $1
+ @language = $3
+ @attributes = {}
+ else
+ raise SyntaxError.new("Error in tag 'code' - Valid syntax: include '[code_file]' as '[language]'")
+ end
+ end
+
+ def render(context)
+ require 'coderay'
+
+ partial = load_cached_partial(context)
+ html = ''
+
+ context.stack do
+ html = CodeRay.scan(partial.root.nodelist.join, @language).div
+ end
+
+ html
+ end
+
+ Liquid::Template.register_tag('code', LiquidCode)
+ end
end
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