Documentation

README.md

+
+# Genesys Anno - Standalone data uploader
+
+Anno is a standalone Java application for managing accession-level data on 
+Genesys PGR - global database on PGR in world's genebanks. Genesys database is 
+accessible at https://www.genesys-pgr.org 
+
+The application allows users to map their Excel, CSV or database SQL queries to Multi-Crop 
+Passport Descriptor format (MCPD) and push the mapped data to Genesys for publication.
+

anno-gui/pom.xml

@@ -183,7 +183,59 @@
 					<encoding>UTF-8</encoding>
 				</configuration>
 			</plugin>
-
+			<plugin>
+				<groupId>org.asciidoctor</groupId>
+				<artifactId>asciidoctor-maven-plugin</artifactId>
+				<version>1.5.3</version>
+				<executions>
+					<execution>
+						<id>output-html</id>
+						<phase>generate-resources</phase>
+						<goals>
+							<goal>process-asciidoc</goal>
+						</goals>
+						<configuration>
+							<backend>html5</backend>
+							<doctype>book</doctype>
+							<sourceHighlighter>coderay</sourceHighlighter>
+							<attributes>
+								<copycss>true</copycss>
+								<!-- <linkcss /> -->
+								<toc>left</toc>
+								<icons>font</icons>
+								<sectanchors>true</sectanchors>
+								<idprefix />
+								<idseparator>-</idseparator>
+								<docinfo1>true</docinfo1>
+							</attributes>
+						</configuration>
+					</execution>
+					<!-- <execution>
+						<id>output-docbook</id>
+						<phase>generate-resources</phase>
+						<goals>
+							<goal>process-asciidoc</goal>
+						</goals>
+						<configuration>
+							<backend>docbook</backend>
+							<doctype>book</doctype>
+						</configuration>
+					</execution> -->
+				</executions>
+				<configuration>
+					<sourceDirectory>src/main/asciidoc</sourceDirectory>
+					<preserveDirectories>true</preserveDirectories>
+					<headerFooter>true</headerFooter>
+					<numbered>true</numbered>
+					<!-- <imagesDir>images</imagesDir> -->
+					<attributes>
+						<buildNumber>${buildNumber}</buildNumber>
+						<projectArtifact>${project.artifactId}</projectArtifact>
+						<projectVersion>${project.version}</projectVersion>
+						<snippets>${snippetsDirectory}</snippets>
+					</attributes>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 </project>
\ No newline at end of file

anno-gui/src/main/asciidoc/index.adoc

+Genesys Anno User Manual
+========================
+December 2015: Commit {buildNumber}
+:revnumber: {projectVersion}
+:doctype: book
+:toc: left
+:toclevels: 5
+:icons: font
+:numbered:
+:source-highlighter: pygments
+:pygments-css: class
+:pygments-linenums-mode: table
+
+
+[[intro]]
+Introduction
+------------
+
+*Anno* is a standalone Java application for managing accession-level data on 
+Genesys PGR - global database on PGR in world's genebanks. Genesys database is 
+accessible at https://www.genesys-pgr.org . 
+
+The application allows users to map their Excel, CSV or database SQL queries to Multi-Crop 
+Passport Descriptor format (MCPD) and push the mapped data to Genesys for publication.
+
+*Genesys Sandbox*, a playground instance of the Genesys
+database, is available for developers and integrators to validate and test their 
+configuration at https://sandbox.genesys-pgr.org
+before pushing data to *live* Genesys servers.
+
+
+
+include::sections/download.adoc[]
+include::sections/workspace.adoc[]
+include::sections/window.adoc[]
+include::sections/settings.adoc[]
+include::sections/datasources.adoc[]
+include::sections/mapping.adoc[]
+include::sections/push.adoc[]
+include::sections/troubleshooting.adoc[]
+include::sections/ack.adoc[]
+

anno-gui/src/main/asciidoc/sections/ack.adoc

+
+[[version]]
+== Version information
+
+* Matija Obreza, Crop Trust: Initial document, January 2016.
+
+=== Acknowledgements
+
+*TBD*