From 64944d6d81cf2c79b78761a95d770c8a8c1fcf9f Mon Sep 17 00:00:00 2001
From: James Agnew <jamesagnew@gmail.com>
Date: Thu, 5 Feb 2015 10:25:18 -0500
Subject: [PATCH] JPA Documentation updates

---
 hapi-fhir-dist/pom.xml                        |  1 +
 hapi-fhir-dist/src/assembly/hapi-fhir-all.xml | 19 ++-------
 .../assembly/hapi-fhir-jpaserver-example.xml  | 35 ++++++++++++++++
 .../org.eclipse.core.resources.prefs          |  2 -
 .../org.eclipse.core.resources.prefs          |  2 -
 src/site/site.xml                             |  9 ++++-
 src/site/xdoc/doc_jpa.xml                     | 40 +++++++++++++++++++
 7 files changed, 87 insertions(+), 21 deletions(-)
 create mode 100644 hapi-fhir-dist/src/assembly/hapi-fhir-jpaserver-example.xml
 create mode 100644 src/site/xdoc/doc_jpa.xml

diff --git a/hapi-fhir-dist/pom.xml b/hapi-fhir-dist/pom.xml
index b6a845c2308..9dd2bfd1632 100644
--- a/hapi-fhir-dist/pom.xml
+++ b/hapi-fhir-dist/pom.xml
@@ -87,6 +87,7 @@
 									<attach>false</attach>
 									<descriptors>
 										<descriptor>${project.basedir}/src/assembly/hapi-fhir-all.xml</descriptor>
+										<descriptor>${project.basedir}/src/assembly/hapi-fhir-jpaserver-example.xml</descriptor>
 									</descriptors>
 								</configuration>
 							</execution>
diff --git a/hapi-fhir-dist/src/assembly/hapi-fhir-all.xml b/hapi-fhir-dist/src/assembly/hapi-fhir-all.xml
index 671f6d703b3..aac691b3fd3 100644
--- a/hapi-fhir-dist/src/assembly/hapi-fhir-all.xml
+++ b/hapi-fhir-dist/src/assembly/hapi-fhir-all.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
 
-	<id>all</id>
+	<id>jpaserver-example</id>
 
 	<formats>
 		<format>zip</format>
@@ -12,24 +12,13 @@
 
 	<fileSets>
 		<fileSet>
-			<directory>${project.basedir}</directory>
+			<directory>${project.basedir}/../hapi-fhir-jpaserver-example</directory>
 			<outputDirectory>/</outputDirectory>
 			<includes>
-				<include>README*</include>
-				<include>LICENSE*</include>
-				<include>NOTICE*</include>
+				<include>pom.xml</include>
+				<include>src/**</include>
 			</includes>
 		</fileSet>
 	</fileSets>
 
-	<dependencySets>
-		<dependencySet>
-			<outputDirectory>/lib</outputDirectory>
-			<useProjectArtifact>true</useProjectArtifact>
-			<unpack>false</unpack>
-			<scope>runtime</scope>
-		</dependencySet>
-	</dependencySets>
-	
-
 </assembly>
diff --git a/hapi-fhir-dist/src/assembly/hapi-fhir-jpaserver-example.xml b/hapi-fhir-dist/src/assembly/hapi-fhir-jpaserver-example.xml
new file mode 100644
index 00000000000..671f6d703b3
--- /dev/null
+++ b/hapi-fhir-dist/src/assembly/hapi-fhir-jpaserver-example.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+
+	<id>all</id>
+
+	<formats>
+		<format>zip</format>
+		<format>tar.bz2</format>
+	</formats>
+
+	<includeBaseDirectory>false</includeBaseDirectory>
+
+	<fileSets>
+		<fileSet>
+			<directory>${project.basedir}</directory>
+			<outputDirectory>/</outputDirectory>
+			<includes>
+				<include>README*</include>
+				<include>LICENSE*</include>
+				<include>NOTICE*</include>
+			</includes>
+		</fileSet>
+	</fileSets>
+
+	<dependencySets>
+		<dependencySet>
+			<outputDirectory>/lib</outputDirectory>
+			<useProjectArtifact>true</useProjectArtifact>
+			<unpack>false</unpack>
+			<scope>runtime</scope>
+		</dependencySet>
+	</dependencySets>
+	
+
+</assembly>
diff --git a/hapi-fhir-jpaserver-base/.settings/org.eclipse.core.resources.prefs b/hapi-fhir-jpaserver-base/.settings/org.eclipse.core.resources.prefs
index e35473ebaf9..29abf999564 100644
--- a/hapi-fhir-jpaserver-base/.settings/org.eclipse.core.resources.prefs
+++ b/hapi-fhir-jpaserver-base/.settings/org.eclipse.core.resources.prefs
@@ -3,6 +3,4 @@ encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
 encoding//src/test/resources=UTF-8
-encoding//target/generated-resources/tinder=UTF-8
-encoding//target/generated-sources/tinder=UTF-8
 encoding/<project>=UTF-8
diff --git a/hapi-fhir-structures-dev/.settings/org.eclipse.core.resources.prefs b/hapi-fhir-structures-dev/.settings/org.eclipse.core.resources.prefs
index e35473ebaf9..29abf999564 100644
--- a/hapi-fhir-structures-dev/.settings/org.eclipse.core.resources.prefs
+++ b/hapi-fhir-structures-dev/.settings/org.eclipse.core.resources.prefs
@@ -3,6 +3,4 @@ encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
 encoding//src/test/resources=UTF-8
-encoding//target/generated-resources/tinder=UTF-8
-encoding//target/generated-sources/tinder=UTF-8
 encoding/<project>=UTF-8
diff --git a/src/site/site.xml b/src/site/site.xml
index 3d838f51842..d61670cbb81 100644
--- a/src/site/site.xml
+++ b/src/site/site.xml
@@ -81,6 +81,7 @@
 			<item name="Logging" href="./doc_logging.html" />
 			<item name="ETags" href="./doc_rest_etag.html" />
 			<item name="Tinder Plugin" href="./doc_tinder.html" />
+			<item name="JPA/Database Server" href="./doc_jpa.html" />
 		</menu>
 
 		<menu name="Community">
@@ -89,10 +90,14 @@
 		</menu>
 
 		<menu name="JavaDocs">
-			<item name="Core API" href="./apidocs/index.html" />
+			<item name="Core API" href="./apidocs/index.html">
+				<item name="Source Code" href="https://github.com/jamesagnew/hapi-fhir" />
+			</item>
 			<item name="Model API (DSTU1)" href="./apidocs-dstu/index.html" />
 			<item name="Model API (DEV)" href="./apidocs-dev/index.html" />
-			<item name="Source Code" href=".https://github.com/jamesagnew/hapi-fhir" />
+			<item name="JPA Server API" href="./apidocs-jpaserver/index.html">
+				<item name="Source Code" href="./xref-jpaserver/index.html" />
+			</item>
 		</menu>
 
 		<menu name="Reports">
diff --git a/src/site/xdoc/doc_jpa.xml b/src/site/xdoc/doc_jpa.xml
new file mode 100644
index 00000000000..b10aa48f5d5
--- /dev/null
+++ b/src/site/xdoc/doc_jpa.xml
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
+
+	<properties>
+		<title>JPA Server - HAPI FHIR</title>
+		<author email="jamesagnew@users.sourceforge.net">James Agnew</author>
+	</properties>
+
+	<body>
+
+		<section name="JPA Server">
+
+			<p>
+				The HAPI FHIR 
+				<a href="./doc_rest_server.html">RestfulServer</a>
+				module can be used to create a FHIR server endpoint against an arbitrary
+				data source, which could be a database of your own design, an existing
+				clinical system, a set of files, or anything else you come up with.
+			</p>
+			<p>
+				HAPI also provides a specific database implementation which can be used to
+				provide a complete RESTful server implementation, backed by a database.
+				HAPI FHIR's JPA module is an implementation of a database storage layer, using
+				the JPA 2.0 API with Hibernate as the recommended implementation.
+			</p>
+			<p>
+				<b>Important Note: </b>
+				This implementation uses a fairly simple table design, with a 
+				single table being used to hold resource bodies (which are stored as 
+				GZipped CLOBs) and a set of tables to hold search indexes, tags, 
+				history details, etc. This design is only one of many possible ways
+				of designing a FHIR server so it is worth considering whether it
+				is appropriate for the problem you are trying to solve.
+			</p>
+			
+		</section>
+
+	</body>
+
+</document>