Merge branch 'release/1.0'

milaboratory · Jan 23, 2015 · f923c39 · f923c39
2 parents d1a3946 + c5cb973
commit f923c39
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diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,6 @@
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
+*.iml
+target
+src/main/java/com/milaboratory/mitools/parsers
diff --git a/README.md b/README.md
@@ -1,5 +1,20 @@
-mitools
+MiTools
 =======
 
 MiTools: yet another Next Generation Sequencing (NGS) data processing tool (based on MiLib)
 
+## License
+
+   Copyright 2015 MiLaboratory.com
+
+   Licensed 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.
diff --git a/pom.xml b/pom.xml
@@ -0,0 +1,222 @@
+<!--
+  ~ Copyright 2015 MiLaboratory.com
+  ~
+  ~ Licensed 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.
+  -->
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>com.milaboratory</groupId>
+    <artifactId>mitools</artifactId>
+    <version>1.0</version>
+    <packaging>jar</packaging>
+    <name>MiTools</name>
+    <url>http://milaboratory.com/</url>
+
+    <parent>
+        <groupId>org.sonatype.oss</groupId>
+        <artifactId>oss-parent</artifactId>
+        <version>7</version>
+        <relativePath></relativePath>
+    </parent>
+
+    <description>
+        Yet another Java library for Next Generation Sequencing (NGS) data processing.
+    </description>
+
+    <licenses>
+        <license>
+            <name>Apache License, Version 2.0</name>
+            <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
+            <distribution>repo</distribution>
+        </license>
+    </licenses>
+
+    <developers>
+        <developer>
+            <id>dbolotin</id>
+            <email>[email protected]</email>
+            <name>Bolotin Dmitriy</name>
+            <organization>MiLaboratory</organization>
+            <organizationUrl>http://milaboratory.com/</organizationUrl>
+            <roles>
+                <role>architect</role>
+                <role>developer</role>
+                <role>tester</role>
+                <role>documentation</role>
+            </roles>
+            <timezone>UTC+04:00</timezone>
+            <url>https://github.com/dbolotin</url>
+        </developer>
+        <developer>
+            <id>PoslavskySV</id>
+            <email>[email protected]</email>
+            <name>Poslavsky Stanislav</name>
+            <organization>MiLaboratory</organization>
+            <organizationUrl>http://milaboratory.com/</organizationUrl>
+            <roles>
+                <role>architect</role>
+                <role>developer</role>
+                <role>tester</role>
+                <role>documentation</role>
+            </roles>
+            <timezone>UTC+04:00</timezone>
+            <url>https://github.com/PoslavskySV</url>
+        </developer>
+        <developer>
+            <id>mikesh</id>
+            <email>[email protected]</email>
+            <name>Mikhail Shugay</name>
+            <organization>MiLaboratory</organization>
+            <organizationUrl>http://milaboratory.com/</organizationUrl>
+            <roles>
+                <role>developer</role>
+                <role>tester</role>
+                <role>documentation</role>
+            </roles>
+            <timezone>UTC+04:00</timezone>
+            <url>https://github.com/mikessh</url>
+        </developer>
+    </developers>
+
+    <dependencies>
+        <dependency>
+            <groupId>com.milaboratory</groupId>
+            <artifactId>milib</artifactId>
+            <version>1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>com.milaboratory</groupId>
+            <artifactId>milib</artifactId>
+            <version>1.0</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.10</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-all</artifactId>
+            <version>1.9.5</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+            <version>1.30</version>
+        </dependency>
+    </dependencies>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+
+    <scm>
+        <connection>scm:git:https://github.com/milaboratory/mitools.git</connection>
+    </scm>
+
+    <issueManagement>
+        <system>YouTrack</system>
+        <url>http://youtrack.milaboratory.com/</url>
+    </issueManagement>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.17</version>
+                <configuration>
+                    <forkMode>never</forkMode>
+                </configuration>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>2.3.2</version>
+                <configuration>
+                    <source>1.7</source>
+                    <target>1.7</target>
+                </configuration>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-antrun-plugin</artifactId>
+                <version>1.7</version>
+                <executions>
+                    <execution>
+                        <phase>process-sources</phase>
+                        <goals>
+                            <goal>run</goal>
+                        </goals>
+                        <configuration>
+                            <tasks>
+                                <delete>
+                                    <fileset dir="${basedir}/src/main/java/" includes="*.tokens"/>
+                                </delete>
+                            </tasks>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>2.3</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <createDependencyReducedPom>false</createDependencyReducedPom>
+                            <minimizeJar>true</minimizeJar>
+                            <filters>
+                                <filter>
+                                    <artifact>com.milaboratory:milib</artifact>
+                                    <includes>
+                                        <include>**</include>
+                                    </includes>
+                                </filter>
+                            </filters>
+                            <transformers>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer">
+                                </transformer>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
+                                    <addHeader>false</addHeader>
+                                </transformer>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>com.milaboratory.mitools.cli.Main</mainClass>
+                                </transformer>
+                            </transformers>
+                            <shadedArtifactAttached>true</shadedArtifactAttached>
+                            <shadedClassifierName>distribution</shadedClassifierName>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>
diff --git a/src/main/java/com/milaboratory/mitools/cli/Action.java b/src/main/java/com/milaboratory/mitools/cli/Action.java
@@ -0,0 +1,27 @@
+/*
+ * Copyright 2015 MiLaboratory.com
+ *
+ * Licensed 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.
+ */
+package com.milaboratory.mitools.cli;
+
+/**
+ * Created by dbolotin on 20/08/14.
+ */
+public interface Action {
+    void go(ActionHelper helper) throws Exception;
+
+    String command();
+
+    ActionParameters params();
+}
diff --git a/src/main/java/com/milaboratory/mitools/cli/ActionHelpProvider.java b/src/main/java/com/milaboratory/mitools/cli/ActionHelpProvider.java
@@ -0,0 +1,23 @@
+/*
+ * Copyright 2015 MiLaboratory.com
+ *
+ * Licensed 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.
+ */
+package com.milaboratory.mitools.cli;
+
+/**
+ * Created by dbolotin on 28/08/14.
+ */
+public interface ActionHelpProvider {
+    void printHelp(StringBuilder builder);
+}
diff --git a/src/main/java/com/milaboratory/mitools/cli/ActionHelper.java b/src/main/java/com/milaboratory/mitools/cli/ActionHelper.java
@@ -0,0 +1,24 @@
+/*
+ * Copyright 2015 MiLaboratory.com
+ *
+ * Licensed 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.
+ */
+package com.milaboratory.mitools.cli;
+
+import java.io.PrintStream;
+
+public interface ActionHelper {
+    PrintStream getDefaultPrintStream();
+
+    String getCommandLineArguments();
+}
diff --git a/src/main/java/com/milaboratory/mitools/cli/ActionParameters.java b/src/main/java/com/milaboratory/mitools/cli/ActionParameters.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright 2015 MiLaboratory.com
+ *
+ * Licensed 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.
+ */
+package com.milaboratory.mitools.cli;
+
+import com.beust.jcommander.Parameter;
+
+public abstract class ActionParameters {
+    @Parameter(names = {"-h", "--help"}, help = true, description = "Displays help for this command.")
+    public Boolean help;
+
+    public boolean help() {
+        return help != null && help;
+    }
+
+    public void validate() {
+    }
+}
diff --git a/src/main/java/com/milaboratory/mitools/cli/ActionParametersParser.java b/src/main/java/com/milaboratory/mitools/cli/ActionParametersParser.java
@@ -0,0 +1,20 @@
+/*
+ * Copyright 2015 MiLaboratory.com
+ *
+ * Licensed 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.
+ */
+package com.milaboratory.mitools.cli;
+
+public interface ActionParametersParser {
+    void parseParameters(String[] args);
+}