revised package development environment.

README.md

@@ -1,27 +1,27 @@
 # BioFormatsImageInfo
 Metadata extraction tool based on Bio-Formats
 
-### Compile
-```shell
-mvn compile
-```
-
-### run
-```shell
-mvn exec:java -Dexec.mainClass=jp.riken.neurodata.tools.BioFormatsImageInfo -Dexec.args="'[path to image file]'"
-```
-
-### make jar package
+### make package
 ```shell
 mvn package
 ```
 
-### run by jar
+### run
 ```shell
-java -jar target/bioformats-imageinfo-1.0.0.jar "[path to image file]"
+./target/dist/bin/bioformats-imageinfo "[path to image file]"
 ```
 
-### run by class
+### run by jar
+```shell
+java -jar ./target/dist/lib/bioformats-imageinfo-1.0.0.jar "[path to image file]"
+```
+
+### run by fat jar
+```shell
+java -jar ./target/bioformats-imageinfo-1.0.0-jar-with-dependencies.jar "[path to image file]"
+```
+
+### library usage
 ```java
 import java.util.LinkedHashMap;
 import java.util.Map;

pom.xml

@@ -11,17 +11,21 @@
   <url>https://neurodata.riken.jp</url>
 
   <properties>
-    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <bio-formats.version>6.10.0</bio-formats.version>
+    <bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
+
     <maven.compiler.source>1.8</maven.compiler.source>
     <maven.compiler.target>1.8</maven.compiler.target>
+
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
   </properties>
 
   <dependencies>
     <dependency>
       <groupId>ome</groupId>
-      <artifactId>bioformats_package</artifactId>
-      <version>6.10.0</version>
-      <type>pom</type>
+      <artifactId>bio-formats-tools</artifactId>
+      <version>${bio-formats.version}</version>
     </dependency>
   </dependencies>
 
@@ -39,8 +43,8 @@
               <goal>copy-dependencies</goal>
             </goals>
             <configuration>
-              <outputDirectory>${project.build.directory}/libs</outputDirectory>
-            </configuration>
+              <overWriteIfNewer>true</overWriteIfNewer>
+           </configuration>
           </execution>
         </executions>
       </plugin>
@@ -52,8 +56,7 @@
           <archive>
             <manifest>
               <addClasspath>true</addClasspath>
-              <classpathPrefix>libs/</classpathPrefix>
-              <mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</mainClass>
+	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
             </manifest>
           </archive>
         </configuration>
@@ -61,14 +64,14 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-assembly-plugin</artifactId>
-        <version>3.4.1</version>
+	<version>3.4.1</version>
         <configuration>
           <descriptorRefs>
             <descriptorRef>jar-with-dependencies</descriptorRef>
           </descriptorRefs>
           <archive>
             <manifest>
-              <mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</mainClass>
+	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
             </manifest>
           </archive>
         </configuration>
@@ -82,6 +85,42 @@
           </execution>
         </executions>
       </plugin>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>appassembler-maven-plugin</artifactId>
+        <version>1.10</version>
+        <configuration>
+          <assembleDirectory>${project.build.directory}/dist</assembleDirectory>
+	  <repositoryLayout>flat</repositoryLayout>
+	  <repositoryName>lib</repositoryName>
+          <programs>
+            <program>
+	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
+	      <id>${project.name}</id>
+            </program>
+          </programs>
+        </configuration>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>assemble</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.owasp</groupId>
+        <artifactId>dependency-check-maven</artifactId>
+        <version>7.1.1</version>
+        <executions>
+          <execution>
+            <goals>
+              <goal>check</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
     </plugins>
   </build>
 
@@ -98,17 +137,16 @@
       <id>central</id>
       <name>Central Repository</name>
       <url>https://repo.maven.apache.org/maven2</url>
-    </repository>
-        <repository>
-      <id>unidata.releases</id>
-      <url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
-      <snapshots><enabled>false</enabled></snapshots>
     </repository>
     <repository>
       <id>ome</id>
       <name>OME Artifactory</name>
       <url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
     </repository>
+    <repository>
+      <id>unidata.releases</id>
+      <url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
+    </repository>
   </repositories>
 
 </project>