neptune 0.1.1 → 0.1.2

data/README

@@ -40,8 +40,7 @@ ts_neptune, you should export the environment variable APPSCALE_HEAD_NODE,
 which should be set to the IP address of the AppScale machine that runs
 the Shadow daemon (a.k.a. the Master AppController). Running
 generate_coverage.sh in the top-level directory will run rcov
-and generate the coverage reports automatically - currently this process
-takes about an hour.
+and generate the coverage reports automatically via unit tests.
 
 Developed by Chris Bunch as part of the AppScale project.
 See LICENSE for the specifics of the New BSD License
@@ -61,11 +60,15 @@ of computation. We would also like to refactor Neptune to use
 symbols instead of instance variables for running jobs: this
 will likely appear in a future release as well.
 
-An academic paper describing Neptune is in the works - check
-in for a link to that as it becomes available.
+Our academic paper on Neptune won best paper at ACM ScienceCloud 2011!
+<a href='http://www.neptune-lang.org/2011/6/Neptune-Picks-up-Best-Paper-at-ScienceCloud-2011'>
+Here's a link</a> to the abstract of the paper and the PDF.
 
 Version History:
 
+November 10, 2011 - 0.1.2 released, adding unit tests and
+refactoring all around.
+
 June 6, 2011 - 0.1.1 released, adding support for code
 written in Go and R
 

data/doc/AppControllerClient.html

@@ -127,6 +127,8 @@
         
           <li><a href="./CommonFunctions.html">CommonFunctions</a></li>
         
+          <li><a href="./Kernel.html">Kernel</a></li>
+        
           <li><a href="./Object.html">Object</a></li>
         
         </ul>
@@ -160,9 +162,11 @@ AppScale Tools, but with non-Neptune SOAP calls removed.</p>
       <div id="conn-attribute-method" class="method-detail">
         <a name="conn"></a>
         
+        <a name="conn="></a>
+        
         <div class="method-heading attribute-method-heading">
           <span class="method-name">conn</span><span
-            class="attribute-access-type">[R]</span>
+            class="attribute-access-type">[RW]</span>
         </div>
 
         <div class="method-description">
@@ -175,9 +179,11 @@ AppScale Tools, but with non-Neptune SOAP calls removed.</p>
       <div id="ip-attribute-method" class="method-detail">
         <a name="ip"></a>
         
+        <a name="ip="></a>
+        
         <div class="method-heading attribute-method-heading">
           <span class="method-name">ip</span><span
-            class="attribute-access-type">[R]</span>
+            class="attribute-access-type">[RW]</span>
         </div>
 
         <div class="method-description">
@@ -190,9 +196,11 @@ AppScale Tools, but with non-Neptune SOAP calls removed.</p>
       <div id="secret-attribute-method" class="method-detail">
         <a name="secret"></a>
         
+        <a name="secret="></a>
+        
         <div class="method-heading attribute-method-heading">
           <span class="method-name">secret</span><span
-            class="attribute-access-type">[R]</span>
+            class="attribute-access-type">[RW]</span>
         </div>
 
         <div class="method-description">
@@ -485,7 +493,7 @@ parameter.</p>
 <span class="ruby-comment"># File lib/app_controller_client.rb, line 96</span>
 def put_input(job_data)
   result = <span class="ruby-string">&quot;&quot;</span>
-  make_call(<span class="ruby-constant">NO_TIMEOUT</span>, false) { 
+  make_call(<span class="ruby-constant">NO_TIMEOUT</span>, false) {
     result = conn.neptune_put_input(job_data, <span class="ruby-ivar">@secret</span>)
   }  
   abort(result) if result =~ <span class="ruby-regexp">/Error:/</span>

data/doc/CommonFunctions.html

@@ -112,6 +112,8 @@
         
           <li><a href="./CommonFunctions.html">CommonFunctions</a></li>
         
+          <li><a href="./Kernel.html">Kernel</a></li>
+        
           <li><a href="./Object.html">Object</a></li>
         
         </ul>
@@ -153,7 +155,7 @@ over code and input files.</p>
         
         <div class="method-heading">
           <span class="method-name">get_from_yaml</span><span
-            class="method-args">(keyname, tag, required=true)</span>
+            class="method-args">(keyname, tag, required=true, file=File, yaml=YAML)</span>
           <span class="method-click-advice">click to toggle source</span>
         </div>
         
@@ -172,17 +174,21 @@ instead.</p>
           <div class="method-source-code"
             id="get_from_yaml-source">
 <pre>
-<span class="ruby-comment"># File lib/common_functions.rb, line 82</span>
-def self.get_from_yaml(keyname, tag, required=true)
-  location_file = <span class="ruby-constant">File</span>.expand_path(&quot;~/.appscale/locations-#{keyname}.yaml&quot;)
+<span class="ruby-comment"># File lib/common_functions.rb, line 91</span>
+def self.get_from_yaml(keyname, tag, required=true, file=<span class="ruby-constant">File</span>, yaml=<span class="ruby-constant">YAML</span>)
+  location_file = file.expand_path(&quot;~/.appscale/locations-#{keyname}.yaml&quot;)
 
-  abort(&quot;An AppScale instance is not currently running with the provided keyname, \&quot;#{keyname}\&quot;.&quot;) unless <span class="ruby-constant">File</span>.exists?(location_file)  
+  if !file.exists?(location_file)
+    abort(<span class="ruby-string">&quot;An AppScale instance is not currently running with the provided&quot;</span> +
+      &quot; keyname, \&quot;#{keyname}\&quot;.&quot;)
+  end
   
   begin
-    tree = <span class="ruby-constant">YAML</span>.load_file(location_file)
+    tree = yaml.load_file(location_file)
   rescue <span class="ruby-constant">ArgumentError</span>
     if required
-      abort(<span class="ruby-string">&quot;The yaml file you provided was malformed. Please correct any errors in it and try again.&quot;</span>)
+      abort(<span class="ruby-string">&quot;The yaml file you provided was malformed. Please correct any&quot;</span> +
+        <span class="ruby-string">&quot; errors in it and try again.&quot;</span>)
     else
       return nil
     end
@@ -190,8 +196,12 @@ def self.get_from_yaml(keyname, tag, required=true)
   
   value = tree[tag]
   
-  bad_yaml_format_msg = &quot;The file #{location_file} is in the wrong format and doesn't contain a #{tag} tag. Please make sure the file is in the correct format and try again&quot;
-  abort(bad_yaml_format_msg) if value.nil? and required
+  if value.nil? and required
+    abort(&quot;The file #{location_file} is in the wrong format and doesn't&quot; +
+      &quot; contain a #{tag} tag. Please make sure the file is in the correct&quot; +
+      <span class="ruby-string">&quot; format and try again.&quot;</span>)
+  end
+
   return value
 end</pre>
           </div>
@@ -210,7 +220,7 @@ end</pre>
         
         <div class="method-heading">
           <span class="method-name">get_secret_key</span><span
-            class="method-args">(keyname, required=true)</span>
+            class="method-args">(keyname, required=true, file=File, yaml=YAML)</span>
           <span class="method-click-advice">click to toggle source</span>
         </div>
         
@@ -227,9 +237,9 @@ function, as the secret is stored in a YAML file.</p>
           <div class="method-source-code"
             id="get_secret_key-source">
 <pre>
-<span class="ruby-comment"># File lib/common_functions.rb, line 107</span>
-def self.get_secret_key(keyname, required=true)
-  return <span class="ruby-constant">CommonFunctions</span>.get_from_yaml(keyname, :secret)
+<span class="ruby-comment"># File lib/common_functions.rb, line 124</span>
+def self.get_secret_key(keyname, required=true, file=<span class="ruby-constant">File</span>, yaml=<span class="ruby-constant">YAML</span>)
+  return <span class="ruby-constant">CommonFunctions</span>.get_from_yaml(keyname, :secret, required, file, yaml)
 end</pre>
           </div>
           
@@ -247,7 +257,7 @@ end</pre>
         
         <div class="method-heading">
           <span class="method-name">scp_file</span><span
-            class="method-args">(local_file_loc, remote_file_loc, target_ip, public_key_loc, is_dir=false)</span>
+            class="method-args">(local_file_loc, remote_file_loc, target_ip, public_key_loc, is_dir=false, file=File, fileutils=FileUtils, kernel=Kernel)</span>
           <span class="method-click-advice">click to toggle source</span>
         </div>
         
@@ -267,43 +277,40 @@ a directory, we append the -r flag to scp as well.</p>
           <div class="method-source-code"
             id="scp_file-source">
 <pre>
-<span class="ruby-comment"># File lib/common_functions.rb, line 37</span>
-def self.scp_file(local_file_loc, remote_file_loc, target_ip, public_key_loc, is_dir=false)
+<span class="ruby-comment"># File lib/common_functions.rb, line 49</span>
+def self.scp_file(local_file_loc, remote_file_loc, target_ip, public_key_loc,
+  is_dir=false, file=<span class="ruby-constant">File</span>, fileutils=<span class="ruby-constant">FileUtils</span>, kernel=<span class="ruby-constant">Kernel</span>)
   cmd = <span class="ruby-string">&quot;&quot;</span>
-  local_file_loc = <span class="ruby-constant">File</span>.expand_path(local_file_loc)
+  local_file_loc = file.expand_path(local_file_loc)
 
   ssh_args = <span class="ruby-string">&quot;-o StrictHostkeyChecking=no 2&gt;&amp;1&quot;</span>
   ssh_args &lt;&lt; <span class="ruby-string">&quot; -r &quot;</span> if is_dir
 
-  if public_key_loc.class == <span class="ruby-constant">Array</span>
-    public_key_loc.each { |key|
-      key = <span class="ruby-constant">File</span>.expand_path(key)
-    }
-    
-    cmd = &quot;scp -i #{public_key_loc.join(' -i ')} #{ssh_args} #{local_file_loc} root@#{target_ip}:#{remote_file_loc}&quot;
-  else
-    public_key_loc = <span class="ruby-constant">File</span>.expand_path(public_key_loc)
-    cmd = &quot;scp -i #{public_key_loc} #{ssh_args} #{local_file_loc} root@#{target_ip}:#{remote_file_loc}&quot;
-  end
-
+  public_key_loc = file.expand_path(public_key_loc)
+  cmd = &quot;scp -i #{public_key_loc} #{ssh_args} #{local_file_loc} root@#{target_ip}:#{remote_file_loc}&quot;
   cmd &lt;&lt; <span class="ruby-string">&quot;; echo $? &gt;&gt; ~/.appscale/retval&quot;</span>
 
-  retval_loc = <span class="ruby-constant">File</span>.expand_path(<span class="ruby-string">&quot;~/.appscale/retval&quot;</span>)
-  <span class="ruby-constant">FileUtils</span>.rm_f(retval_loc)
+  retval_loc = file.expand_path(<span class="ruby-string">&quot;~/.appscale/retval&quot;</span>)
+  fileutils.rm_f(retval_loc)
 
   begin
-    <span class="ruby-constant">Timeout</span>::timeout(-1) { `#{cmd}` }
+    <span class="ruby-constant">Timeout</span>::timeout(-1) { kernel.shell(&quot;#{cmd}&quot;) }
   rescue <span class="ruby-constant">Timeout</span>::<span class="ruby-constant">Error</span>
-    abort(&quot;Remotely copying over files failed. Is the destination machine on and reachable from this computer? We tried the following command:\n\n#{cmd}&quot;)
+    abort(<span class="ruby-string">&quot;Remotely copying over files failed. Is the destination machine&quot;</span> +
+      <span class="ruby-string">&quot; on and reachable from this computer? We tried the following&quot;</span> +
+      &quot; command:\n\n#{cmd}&quot;)
   end
 
   loop {
-    break if <span class="ruby-constant">File</span>.exists?(retval_loc)
+    break if file.exists?(retval_loc)
     sleep(5)
   }
 
-  retval = (<span class="ruby-constant">File</span>.open(retval_loc) { |f| f.read }).chomp
-  abort(&quot;\n\n[#{cmd}] returned #{retval} instead of 0 as expected. Is your environment set up properly?&quot;) if retval != <span class="ruby-string">&quot;0&quot;</span>
+  retval = (file.open(retval_loc) { |f| f.read }).chomp
+  if retval != <span class="ruby-string">&quot;0&quot;</span>
+    abort(&quot;\n\n[#{cmd}] returned #{retval} instead of 0 as expected. Is &quot; +
+      <span class="ruby-string">&quot;your environment set up properly?&quot;</span>)
+  end
   return cmd
 end</pre>
           </div>
@@ -322,7 +329,7 @@ end</pre>
         
         <div class="method-heading">
           <span class="method-name">scp_to_shadow</span><span
-            class="method-args">(local_file_loc, remote_file_loc, keyname, is_dir=false)</span>
+            class="method-args">(local_file_loc, remote_file_loc, keyname, is_dir=false, file=File, get_from_yaml=CommonFunctions.method(:get_from_yaml), scp_file=CommonFunctions.method(:scp_file))</span>
           <span class="method-click-advice">click to toggle source</span>
         </div>
         
@@ -339,12 +346,18 @@ by the Neptune job given, but defaults to ”appscale” if not provided.</p>
           <div class="method-source-code"
             id="scp_to_shadow-source">
 <pre>
-<span class="ruby-comment"># File lib/common_functions.rb, line 24</span>
-def self.scp_to_shadow(local_file_loc, remote_file_loc, keyname, is_dir=false)
-  shadow_ip = <span class="ruby-constant">CommonFunctions</span>.get_from_yaml(keyname, :shadow)
-  ssh_key = <span class="ruby-constant">File</span>.expand_path(&quot;~/.appscale/#{keyname}.key&quot;)
-
-  self.scp_file(local_file_loc, remote_file_loc, shadow_ip, ssh_key, is_dir)
+<span class="ruby-comment"># File lib/common_functions.rb, line 30</span>
+def self.scp_to_shadow(local_file_loc,
+                       remote_file_loc,
+                       keyname,
+                       is_dir=false,
+                       file=<span class="ruby-constant">File</span>,
+                       get_from_yaml=<span class="ruby-constant">CommonFunctions</span>.method(:get_from_yaml),
+                       scp_file=<span class="ruby-constant">CommonFunctions</span>.method(:scp_file))
+
+  shadow_ip = get_from_yaml.call(keyname, :shadow, file)
+  ssh_key = file.expand_path(&quot;~/.appscale/#{keyname}.key&quot;)
+  scp_file.call(local_file_loc, remote_file_loc, shadow_ip, ssh_key, is_dir)
 end</pre>
           </div>
           

data/doc/Kernel.html

@@ -0,0 +1,187 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
+
+  <title>Module: Kernel</title>
+
+  <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+  <script src="./js/jquery.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/thickbox-compressed.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/quicksearch.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="./js/darkfish.js" type="text/javascript"
+    charset="utf-8"></script>
+
+</head>
+<body class="module">
+
+  <div id="metadata">
+    <div id="home-metadata">
+      <div id="home-section" class="section">
+        <h3 class="section-header">
+          <a href="./index.html">Home</a>
+          <a href="./index.html#classes">Classes</a>
+          <a href="./index.html#methods">Methods</a>
+        </h3>
+      </div>
+    </div>
+
+    <div id="file-metadata">
+      <div id="file-list-section" class="section">
+        <h3 class="section-header">In Files</h3>
+        <div class="section-body">
+          <ul>
+          
+            <li><a href="./lib/common_functions_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
+              class="thickbox" title="lib/common_functions.rb">lib/common_functions.rb</a></li>
+          
+          </ul>
+        </div>
+      </div>
+
+      
+    </div>
+
+    <div id="class-metadata">
+
+      <!-- Parent Class -->
+      
+
+      <!-- Namespace Contents -->
+      
+
+      <!-- Method Quickref -->
+      
+      <div id="method-list-section" class="section">
+        <h3 class="section-header">Methods</h3>
+        <ul class="link-list">
+          
+          <li><a href="#method-i-shell">#shell</a></li>
+          
+        </ul>
+      </div>
+      
+
+      <!-- Included Modules -->
+      
+    </div>
+
+    <div id="project-metadata">
+      
+      
+      <div id="fileindex-section" class="section project-section">
+        <h3 class="section-header">Files</h3>
+        <ul>
+        
+          <li class="file"><a href="./LICENSE.html">LICENSE</a></li>
+        
+          <li class="file"><a href="./README.html">README</a></li>
+        
+        </ul>
+      </div>
+      
+
+      <div id="classindex-section" class="section project-section">
+        <h3 class="section-header">Class/Module Index
+          <span class="search-toggle"><img src="./images/find.png"
+            height="16" width="16" alt="[+]"
+            title="show/hide quicksearch" /></span></h3>
+        <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+        <fieldset>
+          <legend>Quicksearch</legend>
+          <input type="text" name="quicksearch" value=""
+            class="quicksearch-field" />
+        </fieldset>
+        </form>
+
+        <ul class="link-list">
+        
+          <li><a href="./AppControllerClient.html">AppControllerClient</a></li>
+        
+          <li><a href="./CommonFunctions.html">CommonFunctions</a></li>
+        
+          <li><a href="./Kernel.html">Kernel</a></li>
+        
+          <li><a href="./Object.html">Object</a></li>
+        
+        </ul>
+        <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+      </div>
+
+      
+    </div>
+  </div>
+
+  <div id="documentation">
+    <h1 class="module">Kernel</h1>
+
+    <div id="description">
+      
+    </div>
+
+    <!-- Constants -->
+    
+
+    <!-- Attributes -->
+    
+
+    <!-- Methods -->
+    
+    <div id="public-instance-method-details" class="method-section section">
+      <h3 class="section-header">Public Instance Methods</h3>
+
+    
+      <div id="shell-method" class="method-detail ">
+        <a name="method-i-shell"></a>
+
+        
+        <div class="method-heading">
+          <span class="method-name">shell</span><span
+            class="method-args">(command)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          
+          
+
+          
+          <div class="method-source-code"
+            id="shell-source">
+<pre>
+<span class="ruby-comment"># File lib/common_functions.rb, line 13</span>
+def shell(command)
+  return `#{command}`
+end</pre>
+          </div>
+          
+        </div>
+
+        
+
+        
+      </div>
+
+    
+    </div>
+  
+
+  </div>
+
+  <div id="validator-badges">
+    <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+    <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+      Rdoc Generator</a> 2</small>.</p>
+  </div>
+
+</body>
+</html>
+