DICE-UNC · michael-conway · Jan 25, 2017 · Jan 26, 2017 · Jan 26, 2017 · Jan 26, 2017
diff --git a/.gitignore b/.gitignore
@@ -1,38 +1,29 @@
-/target
-*.pydevproject
+**/.classpath
+**/.DS_Store
+**/nb-configuration.xml
+**/.springBeans
+**/testing.properties
+*.iml
 .project
+.idea
 .metadata
-.springBeans
-bin/**
-tmp/**
-tmp/**/*
-*.tmp
-*.bak
-*.swp
-*~.nib
-local.properties
-.classpath
-.settings/
-.loadpath
 .DS_Store
-# External tool builders
-.externalToolBuilders/
-
-# Locally stored "Eclipse launch configurations"
-*.launch
-
-# CDT-specific
-.cproject
-
-# PDT-specific
-.buildpath
-
-#Version file
-src/**/RestVersion.java
-
-#removed files
-test-certs/public.pem
-test-certs/private.pem
-test-certs/cakey.pem
-test-certs/cacert.pem
-src/main/resources/admpriv.bin
+Servers
+.settings
+.classpath
+target
+mvn-repo
+bin
+*.war
+*.log
+*/nbactions.xml  
+*.eml
+nbactions.xml
+testing.properties
+*/test-output
+JargonVersion.java
+**/${test.option.mount.basedir}
+*.*~
+**/.project
+**/.settings
+**/target
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -0,0 +1,28 @@
+iRODS license terms and copyright info from the irods site at: https://www.irods.org/index.php/License
+
+License
+iRODS Copyright and Licensing
+
+iRODS is open source software released under a BSD License, see license text in "iRODS License Terms and Conditions" below. 
+The BSD license has been described in very general terms as allowing you to do whatever you want to with the software and 
+source code as long as you acknowledge who wrote it and that, as with any open source software, there is no warranty and you're using the code "as is."
+In the spirit of collaborative open source software, the iRODS community encourages you to communicate with us, letting us know what features you like, 
+features that would be useful, problems, bugs, suggestions, etc., and to perhaps contribute source code.
+The iRODS community has formed the Data Intensive Cyberinfrastructure Foundation, a 501(c)(3) nonprofit corporation established to serve
+ as the home of the iRODS open source community over the long term. If you choose to contribute new code, you'll receive full acknowledgment. All you do is complete the Contributor's Agreement, under which you retain copyright ownership
+  in your code but give a free license to the iRODS nonprofit foundation, allowing your code to be integrated into iRODS and in turn released under the BSD license.
+Note: The above text is an educational overview of iRODS open source licensing, and not intended as legal advice nor is it part of the iRODS license agreement, which is below. As always, for legal advice consult an attorney.
+
+iRODS License Terms and Conditions Notice
+
+Copyright (c) 2005-2011, Regents of the University of California, the University of North Carolina, and the Data Intensive Cyberinfrastructure Foundation 
+All rights reserved.
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+Neither the name of the University of California, San Diego (UCSD) nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT 
+NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
@@ -1,18 +1,23 @@
-# dfc-dataone
-DataONE Member Node Implementation for iRODS
-============================================
 
-Supports DataONE Member Node Tier 1 Implementaion v2.0
+# Project: DataONE Member Node Service
+#### Date: 
+#### Release Version:
+#### git tag: 
+#### Developer: Lisa Stillwell - RENCI,Mike Conway - DICE
 
-Uses: Jargon, Spring, RestEasy
+DataONE Member Node software and supporting libraries
 
-Projects using this code for an iRODS based D1 member node implementation must customize:
 
-1. resources/d1_client.properties
-1. implementation of events/EventLogAO interface
-1. implementation of  id/UniqueIdAO interface
+=======
 
-To Do:
-------
-Develop Tests
+Please go to [[https://github.com/DFC-Incubator/dfc-dataone]] for the latest news and info.
+
+
+## Requirements
+
+* Jargon depends on Java 1.8+
+* Jargon is built using Apache Maven2, see POM for dependencies
+* Jargon supports iRODS 3.0 through iRODS 3.3.1 community, as well as iRODS 4.2.0 consortium
+
+## Libraries
 
diff --git a/dataone-node/Dockerfile b/dataone-node/Dockerfile
@@ -0,0 +1,18 @@
+FROM tomcat:jre8-alpine
+LABEL organization="RENCI"
+LABEL maintainer="[email protected]"
+LABEL description="DFC Member Node"
+ADD target/dataone-node.war /usr/local/tomcat/webapps/
+ADD runit.sh /
+ADD context.xml /usr/local/tomcat/conf
+CMD ["/runit.sh"]
+#CMD ["sh"]
+# build: docker build -t diceunc/dataone:4.2.1.0-SNAPSHOT .
+
+
+# run:  docker run -i -p 8080:8080 -v /etc/irods-ext:/etc/irods-ext -v /etc/irods-ext/d1plugins:/etc/irods-ext/d1plugins -v /home/mcc/webdavcert:/tmp/cert  --add-host irods420.irodslocal:172.16.250.101 diceunc/dataone:4.2.1.0-SNAPSHOT
+
+# to add addl libs -v /etc/irods-ext/d1libs:/tmp/lib
+
+
+#  docker run -i -p 8080:8080 -v /home/mcc/external:/tmp/lib -v /etc/irods-ext:/etc/irods-ext -v /home/mcc/d1plugin:/etc/irods-ext/d1plugins -v /home/mcc/webdavcert:/tmp/cert  --add-host irods420.irodslocal:172.16.250.101 diceunc/dataone:4.2.1.0-SNAPSHOT
diff --git a/dataone-node/README.md b/dataone-node/README.md
@@ -0,0 +1,24 @@
+
+# Project: DataONE Node
+#### Date: 
+#### Release Version:
+#### git tag: 
+#### Developer: Lisa Stillwell - RENCI, Mike Conway - DFC/RENCI
+
+## News
+
+
+## Requirements
+
+* Depends on Java 1.8+
+* Built using Apache Maven2, see POM for dependencies
+* Supports iRODS 3.0 through iRODS 3.3.1 community, as well as iRODS 4.2.0 consortium
+
+## Running
+
+```
+mvn spring-boot:run
+
+```
+
+## Changes
diff --git a/dataone-node/TESTING.md b/dataone-node/TESTING.md
@@ -0,0 +1,53 @@
+# Testing setup notes
+
+### maven profile
+
+add the following to your maven settings.xml profile in your home/.m2 directory
+
+```xml  
+
+<profile>
+			<id>dataone</id>
+			<properties>
+				<test.plugin.jar.location>/home/mconway/temp/dataonejar</test.plugin.jar.location>
+			</properties>
+		</profile>
+
+
+
+```
+
+That .jar directory will be the place to put the .jar files for your pid and event service plugins.  These are discovered by the PluginDiscoveryService. 
+
+### build and place your plugin jars in the test plugin jar location
+
+Dummy plugins are being built, including the dummy-event-service-impl included in this repo.  These dummy jar files can be copied out of the target directory of the dummy subproject 
+in order to run the unit and integration tests that depend on successful lookup
+
+### sample unit test
+
+Check out the PluginDiscoveryServiceTest unit test for examples of testing the loading of a plugin, as in this simple case:
+
+```java
+
+@Test
+	public void testInstanceEventService() throws Exception {
+		IRODSAccessObjectFactory aof = Mockito
+				.mock(IRODSAccessObjectFactory.class);
+		PublicationContext publicationContext = new PublicationContext();
+		RestConfiguration restConfiguration = new RestConfiguration();
+		restConfiguration.setPluginJarLocation(dataOneTestHelper
+				.getPluginJarLocation(dataOneProperties));
+		publicationContext.setRestConfiguration(restConfiguration);
+		publicationContext.setIrodsAccessObjectFactory(aof);
+		PluginDiscoveryService pluginDiscoveryService = new PluginDiscoveryService();
+		pluginDiscoveryService.setPublicationContext(publicationContext);
+		pluginDiscoveryService.init();
+
+		EventServiceAO eventServiceAO = pluginDiscoveryService
+				.instanceEventService();
+		Assert.assertNotNull("no eventServiceAO", eventServiceAO);
+	}
+
+
+```
diff --git a/dataone-node/context.xml b/dataone-node/context.xml
@@ -0,0 +1,36 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+  Licensed to the Apache Software Foundation (ASF) under one or more
+  contributor license agreements.  See the NOTICE file distributed with
+  this work for additional information regarding copyright ownership.
+  The ASF licenses this file to You under the Apache License, Version 2.0
+  (the "License"); you may not use this file except in compliance with
+  the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+-->
+<!-- The contents of this file will be loaded for each web application -->
+<Context>
+    <JarScanner scanManifest="false"/>
+    <!-- Default set of monitored resources. If one of these changes, the    -->
+    <!-- web application will be reloaded.                                   -->
+    <WatchedResource>WEB-INF/web.xml</WatchedResource>
+    <WatchedResource>${catalina.base}/conf/web.xml</WatchedResource>
+
+    <!-- Uncomment this to disable session persistence across Tomcat restarts -->
+    <!--
+    <Manager pathname="" />
+    -->
+
+    <!-- Uncomment this to enable Comet connection tacking (provides events
+         on session expiration as well as webapp lifecycle) -->
+    <!--
+    <Valve className="org.apache.catalina.valves.CometConnectionManagerValve" />
+    -->
+</Context>
diff --git a/src/main/resources/d1client.properties → ...ne-node/etc/irods-ext/d1client.properties b/src/main/resources/d1client.properties → ...ne-node/etc/irods-ext/d1client.properties
@@ -57,3 +57,23 @@ irods.dataone.events.elasticsearch.searchindex=databook
 irods.dataone.events.elasticsearch.searchtype=entity
 irods.dataone.events.elasticsearch.cluster.name=databookIndexer
 
+# REST Props
+irods.host=localhost
+irods.port=1247
+irods.zone=tempZone
+# user and password for dataone user
+irods.username=test1
+irods.password=test
+# STANDARD | PAM AUTH
+auth.type=STANDARD
+default.storage.resource=
+# web.interface.url is currently optional and not fully implemented, it can be left blank.
+# sets jargon ssl negotiation policy for the client. Leaving to DONT_CARE defers to the server, and is recommended
+# NO_NEGOTIATION, CS_NEG_REFUSE, CS_NEG_REQUIRE, CS_NEG_DONT_CARE
+ssl.negotiation.policy=CS_NEG_DONT_CARE
+# location for discovered plug-ins
+plugin.jar.location=/etc/irods-ext/d1plugins
+
+plugin.factory.pid=
+plugin.factory.event=org.irods.jargon.dataone.events.defdb.DefaultEventServiceFactory
+plugin.factory.repo=