Merge pull request #9 from hms-dbmi/development-1.0

Development 1.0
hms-dbmi · May 20, 2016 · 07559d2 · 07559d2
2 parents 191b3d5 + 42b4647
commit 07559d2
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Showing 456 changed files with 59,104 additions and 10,751 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,3 +12,7 @@
 
 .settings/org.eclipse.wst.common.project.facet.core.xml
 /model/
+
+.settings/org.eclipse.m2e.wtp.prefs
+
+.settings/org.eclipse.wst.validation.prefs
diff --git a/javadoc/allclasses-frame.html b/javadoc/allclasses-frame.html
diff --git a/javadoc/allclasses-noframe.html b/javadoc/allclasses-noframe.html
diff --git a/javadoc/constant-values.html b/javadoc/constant-values.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_45) on Thu Dec 10 16:47:35 CST 2015 -->
+<!-- Generated by javadoc (1.8.0_45) on Thu May 19 09:41:02 EDT 2016 -->
 <title>Constant Field Values</title>
-<meta name="date" content="2015-12-10">
+<meta name="date" content="2016-05-19">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>

diff --git a/javadoc/deprecated-list.html b/javadoc/deprecated-list.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_45) on Thu Dec 10 16:47:36 CST 2015 -->
+<!-- Generated by javadoc (1.8.0_45) on Thu May 19 09:41:02 EDT 2016 -->
 <title>Deprecated List</title>
-<meta name="date" content="2015-12-10">
+<meta name="date" content="2016-05-19">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>

diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/IRCTApplication.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/IRCTApplication.html
diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/action/Action.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/action/Action.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_45) on Thu Dec 10 16:47:35 CST 2015 -->
+<!-- Generated by javadoc (1.8.0_45) on Thu May 19 09:41:01 EDT 2016 -->
 <title>Action</title>
-<meta name="date" content="2015-12-10">
+<meta name="date" content="2016-05-19">
 <link rel="stylesheet" type="text/css" href="../../../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../../../script.js"></script>
 </head>
@@ -18,7 +18,7 @@
     catch(err) {
     }
 //-->
-var methods = {"i0":6,"i1":6};
+var methods = {"i0":6,"i1":6,"i2":6,"i3":6};
 var tabs = {65535:["t0","All Methods"],2:["t2","Instance Methods"],4:["t3","Abstract Methods"]};
 var altColor = "altColor";
 var rowColor = "rowColor";
@@ -50,7 +50,7 @@
 <div class="subNav">
 <ul class="navList">
 <li>Prev&nbsp;Class</li>
-<li><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/BinaryTreeExecutable.html" title="interface in edu.harvard.hms.dbmi.bd2k.irct.action"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
+<li><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/ActionStatus.html" title="enum in edu.harvard.hms.dbmi.bd2k.irct.action"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
 </ul>
 <ul class="navList">
 <li><a href="../../../../../../../index.html?edu/harvard/hms/dbmi/bd2k/irct/action/Action.html" target="_top">Frames</a></li>
@@ -100,12 +100,8 @@ <h2 title="Interface Action" class="title">Interface Action</h2>
 <ul class="blockList">
 <li class="blockList">
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-<dt>All Known Subinterfaces:</dt>
-<dd><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/join/JoinAction.html" title="interface in edu.harvard.hms.dbmi.bd2k.irct.action.join">JoinAction</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/process/ProcessAction.html" title="interface in edu.harvard.hms.dbmi.bd2k.irct.action.process">ProcessAction</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/query/QueryAction.html" title="interface in edu.harvard.hms.dbmi.bd2k.irct.action.query">QueryAction</a></dd>
-</dl>
-<dl>
 <dt>All Known Implementing Classes:</dt>
-<dd><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/process/ExecuteProcess.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action.process">ExecuteProcess</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/query/ExecuteQuery.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action.query">ExecuteQuery</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/join/FullOuterJoin.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action.join">FullOuterJoin</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/join/InnerJoin.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action.join">InnerJoin</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/join/LeftOuterJoin.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action.join">LeftOuterJoin</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/join/RightOuterJoin.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action.join">RightOuterJoin</a></dd>
+<dd><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/JoinAction.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action">JoinAction</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/ProcessAction.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action">ProcessAction</a>, <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/QueryAction.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.action">QueryAction</a></dd>
 </dl>
 <hr>
 <br>
@@ -136,15 +132,27 @@ <h3>Method Summary</h3>
 <th class="colLast" scope="col">Method and Description</th>
 </tr>
 <tr id="i0" class="altColor">
-<td class="colFirst"><code><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/result/ResultSet.html" title="interface in edu.harvard.hms.dbmi.bd2k.irct.model.result">ResultSet</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/Action.html#getResults--">getResults</a></span>()</code>
-<div class="block">Gets the results</div>
+<td class="colFirst"><code><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/result/Result.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.result">Result</a></code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/Action.html#getResults-edu.harvard.hms.dbmi.bd2k.irct.model.security.SecureSession-">getResults</a></span>(<a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/security/SecureSession.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.security">SecureSession</a>&nbsp;secureSession)</code>
+<div class="block">Returns the results from an action</div>
 </td>
 </tr>
 <tr id="i1" class="rowColor">
+<td class="colFirst"><code><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/ActionStatus.html" title="enum in edu.harvard.hms.dbmi.bd2k.irct.action">ActionStatus</a></code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/Action.html#getStatus--">getStatus</a></span>()</code>
+<div class="block">Returns the actions status</div>
+</td>
+</tr>
+<tr id="i2" class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/Action.html#run-edu.harvard.hms.dbmi.bd2k.irct.model.security.SecureSession-">run</a></span>(<a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/security/SecureSession.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.security">SecureSession</a>&nbsp;secureSession)</code>
+<div class="block">Run the given action in a secure session if required</div>
+</td>
+</tr>
+<tr id="i3" class="rowColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/Action.html#run--">run</a></span>()</code>
-<div class="block">Runs the given action</div>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/Action.html#updateActionParams-java.util.Map-">updateActionParams</a></span>(java.util.Map&lt;java.lang.String,<a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/result/Result.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.result">Result</a>&gt;&nbsp;updatedParams)</code>
+<div class="block">Updates the parameters of the action with the new information.</div>
 </td>
 </tr>
 </table>
@@ -162,35 +170,67 @@ <h3>Method Summary</h3>
 <!--   -->
 </a>
 <h3>Method Detail</h3>
-<a name="run--">
+<a name="run-edu.harvard.hms.dbmi.bd2k.irct.model.security.SecureSession-">
 <!--   -->
 </a>
 <ul class="blockList">
 <li class="blockList">
 <h4>run</h4>
-<pre>void&nbsp;run()
+<pre>void&nbsp;run(<a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/security/SecureSession.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.security">SecureSession</a>&nbsp;secureSession)
   throws <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/exception/ResourceInterfaceException.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.exception">ResourceInterfaceException</a></pre>
-<div class="block">Runs the given action</div>
+<div class="block">Run the given action in a secure session if required</div>
 <dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>secureSession</code> - A secure session (Null if not needed or set)</dd>
 <dt><span class="throwsLabel">Throws:</span></dt>
-<dd><code><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/exception/ResourceInterfaceException.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.exception">ResourceInterfaceException</a></code> - An error occurred</dd>
+<dd><code><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/exception/ResourceInterfaceException.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.exception">ResourceInterfaceException</a></code> - A resource interface exception occurred</dd>
 </dl>
 </li>
 </ul>
-<a name="getResults--">
+<a name="updateActionParams-java.util.Map-">
 <!--   -->
 </a>
-<ul class="blockListLast">
+<ul class="blockList">
+<li class="blockList">
+<h4>updateActionParams</h4>
+<pre>void&nbsp;updateActionParams(java.util.Map&lt;java.lang.String,<a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/result/Result.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.result">Result</a>&gt;&nbsp;updatedParams)</pre>
+<div class="block">Updates the parameters of the action with the new information. This is typically used in chained actions.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>updatedParams</code> - Updated parameters of an action</dd>
+</dl>
+</li>
+</ul>
+<a name="getResults-edu.harvard.hms.dbmi.bd2k.irct.model.security.SecureSession-">
+<!--   -->
+</a>
+<ul class="blockList">
 <li class="blockList">
 <h4>getResults</h4>
-<pre><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/result/ResultSet.html" title="interface in edu.harvard.hms.dbmi.bd2k.irct.model.result">ResultSet</a>&nbsp;getResults()
-              throws <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/exception/ResourceInterfaceException.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.exception">ResourceInterfaceException</a></pre>
-<div class="block">Gets the results</div>
+<pre><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/result/Result.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.result">Result</a>&nbsp;getResults(<a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/model/security/SecureSession.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.model.security">SecureSession</a>&nbsp;secureSession)
+           throws <a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/exception/ResourceInterfaceException.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.exception">ResourceInterfaceException</a></pre>
+<div class="block">Returns the results from an action</div>
 <dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>secureSession</code> - A secure session (Null if not needed or set)</dd>
 <dt><span class="returnLabel">Returns:</span></dt>
-<dd>Results ResultSet</dd>
+<dd>The results of the action</dd>
 <dt><span class="throwsLabel">Throws:</span></dt>
-<dd><code><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/exception/ResourceInterfaceException.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.exception">ResourceInterfaceException</a></code> - An error occurred</dd>
+<dd><code><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/exception/ResourceInterfaceException.html" title="class in edu.harvard.hms.dbmi.bd2k.irct.exception">ResourceInterfaceException</a></code> - A resource interface exception occurred</dd>
+</dl>
+</li>
+</ul>
+<a name="getStatus--">
+<!--   -->
+</a>
+<ul class="blockListLast">
+<li class="blockList">
+<h4>getStatus</h4>
+<pre><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/ActionStatus.html" title="enum in edu.harvard.hms.dbmi.bd2k.irct.action">ActionStatus</a>&nbsp;getStatus()</pre>
+<div class="block">Returns the actions status</div>
+<dl>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>Action Status</dd>
 </dl>
 </li>
 </ul>
@@ -223,7 +263,7 @@ <h4>getResults</h4>
 <div class="subNav">
 <ul class="navList">
 <li>Prev&nbsp;Class</li>
-<li><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/BinaryTreeExecutable.html" title="interface in edu.harvard.hms.dbmi.bd2k.irct.action"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
+<li><a href="../../../../../../../edu/harvard/hms/dbmi/bd2k/irct/action/ActionStatus.html" title="enum in edu.harvard.hms.dbmi.bd2k.irct.action"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
 </ul>
 <ul class="navList">
 <li><a href="../../../../../../../index.html?edu/harvard/hms/dbmi/bd2k/irct/action/Action.html" target="_top">Frames</a></li>