update license and code headers

CONTRIBUTING.rst

@@ -0,0 +1,85 @@
+=================
+How to Contribute
+=================
+
+We welcome community contributions to the caDSR cgMDR project.
+Your contributions back to this repository will allow the broader
+research community to benefit from your work and will allow your
+enhancements to be integrated with those of others.  There are a few
+guidelines that we ask contributors to follow so that we can have a
+chance of keeping on top of things.
+
+---------------
+Getting Started
+---------------
+
+* Make sure you have a `GitHub Account`_.
+
+* Fork the repository on GitHub to publish any proposed changes
+
+* Submit a ticket for your issue at [tracker] (http://gforge.nci.nih.gov/frs/?group_id=541),
+  assuming one does not already exist.
+
+  - Click [here] (https://gforge.nci.nih.gov/account/register.php) to get a new account.
+  - Clearly describe the issue including steps to reproduce when it is a bug.
+  - Make sure you fill in the earliest version that you know has the issue.
+
+.. _`GitHub Account`: https://github.com/signup/free
+
+--------------
+Making Changes
+--------------
+
+* Create a topic branch from where you want to base your work.
+
+  - This is usually the master branch.
+  - Only target release branches if you are certain your fix must be
+    on that branch.
+  - To quickly create a topic branch based on master::
+
+     git checkout -b fix/master/my_contribution master
+
+    Please avoid working directly on the master branch.
+
+* Make commits of logical units.
+
+* Please provide tests and documentation with your changes.
+
+* Check for unnecessary whitespace with ``git diff --check`` before committing.
+
+* Follow the `NCIP Good Practices for Commit Messages`_.
+  Start with a one-line summary followed by a blank line followed by a
+  detailed free-form description.
+
+.. _`NCIP Good Practices for Commit Messages`: https://github.com/NCIP/ncip.github.com/wiki/Good-Practices#wiki-commit-messages
+
+------------------
+Submitting Changes
+------------------
+
+* In general, we require that the OSI-approved `BSD 3-Clause License`_
+  be applied to code contributions.  There may be cases, however, that
+  warrant the use of an alternate OSI-approved license and we will
+  evaluate this situations case-by-case.
+
+* Push your changes to a topic branch in your fork of the repository.
+
+* Submit a pull request to the repository in the NCIP organization.
+
+.. If the project uses an issue tracker, use the next bullet.
+   Otherwise, remove the next bullet.  Delete this note either way.
+
+* Update your [tracker] (http://gforge.nci.nih.gov/frs/?group_id=541) ticket to mark that you have submitted
+  code and are ready for it to be reviewed.
+
+  - Include a link to the pull request in the ticket
+
+.. _`BSD-3-Clause License`: http://opensource.org/licenses/BSD-3-Clause
+
+--------------------
+Additional Resources
+--------------------
+
+For help learning Git and Github, see the `NCIP Learning Resources`_.
+
+.. _`NCIP Learning Resources`: https://github.com/NCIP/ncip.github.com/wiki/Learning-Resources

NOTICE

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+cgMDR-NCI-UK
+Copyright 2009, Oracle Inc. 
+
+This project is distributed under the BSD 3-Clause License.
+Please see LICENSE file for details.
+
+This project was developed as part of the NCI caBIG initiative.
+
+In 2013, as part of the National Cancer Informatics Program (NCIP) Open Development Initiative, 
+the cgMDR-NCI-UK source code was migrated to GitHub to allow further development by the broader community

README.md

@@ -0,0 +1,16 @@
+Welcome to the caDSR cgMDR-NCI-UK Project!
+=====================================
+
+cgMDR has tools enabling semantic annotation from its own metadata repository but also can resolve metadata and terminologies from remote metadata resources such as the caDSR and EVS.
+
+The caDSR cgMDR-NCI-UK is distributed under the BSD 3-Clause License.
+Please see the NOTICE and LICENSE files for details.
+
+You will find more details about the caDSR cgMDR-NCI-UK in the following links:
+ * [Community Wiki] (https://wiki.nci.nih.gov/x/-bWl)
+ * [Code Repository] (https://github.com/NCIP/cadsr-cgmdr-nci-uk)
+ * [Issue Tracker] (https://gforge.nci.nih.gov/tracker/?group_id=541)
+ * [Downloads] (https://gforge.nci.nih.gov/frs/?group_id=541)
+
+
+Please join us in further developing and improving the caDSR cgMDR-NCI-UK project.

atom-services.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
+
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <atom-services xmlns="http://www.exist-db.org/Vocabulary/AtomConfiguration/2006/1/0">
 <module name="edit" class="org.exist.atom.modules.AtomProtocol"/>
 <module name="content" class="org.exist.atom.modules.AtomFeeds"/>

backup.properties

@@ -1,3 +1,10 @@
+#L
+# Copyright Oracle Inc
+#
+# Distributed under the OSI-approved BSD 3-Clause License.
+# See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+#L
+
 # properties used for backup/restore
 
 # XMLDB driver

build.properties

@@ -1,3 +1,10 @@
+#L
+# Copyright Oracle Inc
+#
+# Distributed under the OSI-approved BSD 3-Clause License.
+# See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+#L
+
 # $Id: build.properties 7802 2008-05-25 09:57:21Z dizzzz $
 project.name = eXist
 project.version = 1.2.2

build.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist 1.x build file                                                    -->
 <!-- ======================================================================= -->

build/scripts/build-impl.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist build file                                                        -->
 <!-- ======================================================================= -->

build/scripts/cocoon/build.properties

@@ -1,3 +1,10 @@
+#L
+# Copyright Oracle Inc
+#
+# Distributed under the OSI-approved BSD 3-Clause License.
+# See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+#L
+
 #Mon Oct 16 22:56:52 CEST 2006
 
 # Edit to point to the directory where you unpacked the Cocoon source distribution

build/scripts/cocoon/build.xml

@@ -1,3 +1,10 @@
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!--
     Inject eXist as a Cocoon block into the Cocoon source distribution.
     Execute this script with

build/scripts/cruisecontrol/config.xml

@@ -1,3 +1,10 @@
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <cruisecontrol>
 <!-- ********************************************************** -->
 <!--

build/scripts/cruisecontrol/projects/build.exist.xml

@@ -1,3 +1,10 @@
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <project name="exist" default="nothing" basedir=".">
 
     <property name="exist.target.dir" location="${current.checkout.dir}/exist${project-suffix}"/>

build/scripts/cruisecontrol/projects/build.xml

@@ -1,3 +1,10 @@
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <project name="build" default="nothing" basedir=".">
     <taskdef name="svn" classname="org.tigris.subversion.svnant.SvnTask"/>
     <property file="${build.properties.file}"/>

build/scripts/demoserver.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist build file :  Create HTML files for docs on http://exist-db.org   -->
 <!-- ======================================================================= -->

build/scripts/dist.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0" encoding="iso-8859-1" ?>
+
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- $Id: dist.xml 7071 2007-12-20 16:12:21Z dizzzz $ -->
 <project basedir="../.." default="dist" name="dist">
 

build/scripts/installer.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
+
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist build file : Build installer                                      -->
 <!-- ======================================================================= -->

build/scripts/jarsigner.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0"?>
+
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!--
     Dedicated ant "build" file for signing eXist jar files.
     

build/scripts/junit.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist build file : Run jUnit tests                                      -->
 <!-- ======================================================================= -->

build/scripts/minimal.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
+
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- $Id: minimal.xml 5616 2007-04-07 13:19:18Z dizzzz $ -->
 <project name="minimal" basedir="../.." default="dist-minimal">
 

build/scripts/performance.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist build file : Run jUnit tests                                      -->
 <!-- ======================================================================= -->

build/scripts/quality.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="iso-8859-1" ?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- 
 		Test the quality of code with PMD, JDepend, ...
 		Designed to be imported by main build.xml , 

build/scripts/soap.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist build file : Axis SOAP                                            -->
 <!-- ======================================================================= -->

build/scripts/subversion.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <!-- ======================================================================= -->
 <!-- eXist build file : Subversion                                            -->
 <!-- ======================================================================= -->

cancergrid/addins/QueryServiceAddIn/ExcelQueryServiceAddIn/ExcelQueryServiceRibbon.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
+
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <customUI xmlns="http://schemas.microsoft.com/office/2006/01/customui" onLoad="Ribbon_Load">
   <ribbon>
     <tabs>

cancergrid/addins/QueryServiceAddIn/ExcelQueryServiceAddIn/ThisAddIn.Designer.xml

@@ -1,3 +1,10 @@
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <hostitem:hostItem hostitem:baseType="Microsoft.Office.Tools.AddIn" hostitem:interfaceType="Microsoft.VisualStudio.Tools.Office.IOfficeEntryPoint" hostitem:namespace="ExcelQueryServiceAddIn" hostitem:className="ThisAddIn" hostitem:identifier="ThisAddIn" hostitem:primaryCookie="AddIn" hostitem:master="true" hostitem:startupIndex="0" xmlns:hostitem="http://schemas.microsoft.com/2004/VisualStudio/Tools/Applications/HostItem.xsd">
   <hostitem:hostObject hostitem:name="Application" hostitem:identifier="Application" hostitem:type="Microsoft.Office.Interop.Excel.Application" hostitem:cookie="Application" hostitem:modifier="Internal" />
   <hostitem:hostControl hostitem:name="CustomTaskPanes" hostitem:identifier="CustomTaskPanes" hostitem:type="Microsoft.Office.Tools.CustomTaskPaneCollection" hostitem:primaryCookie="CustomTaskPanes" hostitem:modifier="Internal" />

cancergrid/addins/QueryServiceAddIn/InfoPathQueryServiceAddIn/ThisAddIn.Designer.xml

@@ -1,3 +1,10 @@
+<!--L
+  Copyright Oracle Inc
+
+  Distributed under the OSI-approved BSD 3-Clause License.
+  See http://ncip.github.com/cadsr-cgmdr-nci-uk/LICENSE.txt for details.
+L-->
+
 <hostitem:hostItem hostitem:baseType="Microsoft.Office.Tools.AddIn" hostitem:interfaceType="Microsoft.VisualStudio.Tools.Office.IOfficeEntryPoint" hostitem:namespace="InfoPathQueryServiceAddIn" hostitem:className="ThisAddIn" hostitem:identifier="ThisAddIn" hostitem:primaryCookie="AddIn" hostitem:master="true" hostitem:startupIndex="0" xmlns:hostitem="http://schemas.microsoft.com/2004/VisualStudio/Tools/Applications/HostItem.xsd">
   <hostitem:hostObject hostitem:name="Application" hostitem:identifier="Application" hostitem:type="Microsoft.Office.Interop.InfoPath.Application" hostitem:cookie="Application" hostitem:modifier="Internal" />
   <hostitem:hostControl hostitem:name="CustomTaskPanes" hostitem:identifier="CustomTaskPanes" hostitem:type="Microsoft.Office.Tools.CustomTaskPaneCollection" hostitem:primaryCookie="CustomTaskPanes" hostitem:modifier="Internal" />