Move source to standard Gradle layout

.project

@@ -6,18 +6,34 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
-			<name>org.python.pydev.PyDevBuilder</name>
+			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.python.pydev.pythonNature</nature>
+		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
 </projectDescription>

build.gradle

@@ -13,7 +13,6 @@ var DEFAULT_URL = "https://ci.kbase.us/services/narrative_method_store/rpc"
 var LOC_NMS_SPEC = "$rootDir/NarrativeMethodStore.spec"
 var LOC_DOC_HTML = "$rootDir/docshtml"
 
-// TODO NOW run tests from Eclipse w/o specifying classpath manually & remove sourceSets & classpath
 // TODO BUILD use jitpacked jars when available
 
 repositories {
@@ -130,10 +129,10 @@ task sdkCompileLibs {
 }
 
 task sdkCompileJava {
-	// TODO GRADLE is there a variable for src/main/java when we move the code locations?
+	// TODO GRADLE is there a variable for src/main/java?
 	var cmd = "kb-sdk compile " +
 				"--java " +
-				"--javasrc $rootDir/src " +
+				"--javasrc $rootDir/src/main/java " +
 				"--javasrv " +
 				"--out . " +
 				"--url $DEFAULT_URL " + 
@@ -152,26 +151,6 @@ task sdkCompile {
 	dependsOn sdkCompileLibs
 }
 
-// Custom java project layout
-sourceSets {
-	main {
-		java {
-			srcDirs = ["src"]
-			exclude '**/test/**'
-		}
-	}
-	test {
-		java {
-			srcDirs = ["src"]
-			include '**/test/**'
-		}
-		resources {
-			srcDirs = ["src"]
-			include "**/*.properties"
-		}
-	}
-}
-
 configurations {
 	// can't directly access testImplementation, so extend and access
 	testimpl.extendsFrom testImplementation

src/us/kbase/narrativemethodstore/test/FullServerTest.java → src/test/java/us/kbase/test/narrativemethodstore/FullServerTest.java

@@ -1,4 +1,4 @@
-package us.kbase.narrativemethodstore.test;
+package us.kbase.test.narrativemethodstore;
 
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.assertEquals;
@@ -38,7 +38,7 @@
 import us.kbase.common.service.Tuple4;
 import us.kbase.narrativemethodstore.*;
 import us.kbase.narrativemethodstore.db.DynamicRepoDB;
-import us.kbase.narrativemethodstore.db.mongo.test.MongoDBHelper;
+import us.kbase.test.narrativemethodstore.db.mongo.MongoDBHelper;
 
 /**
  * Client-server JSON-RPC test for Narrative Method Store.

src/us/kbase/narrativemethodstore/db/test/NarrativeMethodDataTest.java → src/test/java/us/kbase/test/narrativemethodstore/db/NarrativeMethodDataTest.java

@@ -1,4 +1,4 @@
-package us.kbase.narrativemethodstore.db.test;
+package us.kbase.test.narrativemethodstore.db;
 
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.CoreMatchers.nullValue;

src/us/kbase/narrativemethodstore/db/test/ServiceUrlTemplateEvaluaterTest.java → src/test/java/us/kbase/test/narrativemethodstore/db/ServiceUrlTemplateEvaluaterTest.java

@@ -1,4 +1,4 @@
-package us.kbase.narrativemethodstore.db.test;
+package us.kbase.test.narrativemethodstore.db;
 
 import junit.framework.Assert;
 

src/us/kbase/narrativemethodstore/db/test/ValidatorTest.java → src/test/java/us/kbase/test/narrativemethodstore/db/ValidatorTest.java

@@ -1,4 +1,4 @@
-package us.kbase.narrativemethodstore.db.test;
+package us.kbase.test.narrativemethodstore.db;
 
 import java.io.File;
 import java.util.Collections;

src/us/kbase/narrativemethodstore/db/mongo/test/MongoDBHelper.java → src/test/java/us/kbase/test/narrativemethodstore/db/mongo/MongoDBHelper.java

@@ -1,4 +1,4 @@
-package us.kbase.narrativemethodstore.db.mongo.test;
+package us.kbase.test.narrativemethodstore.db.mongo;
 
 import java.io.File;
 import java.io.IOException;

src/us/kbase/narrativemethodstore/db/mongo/test/MongoDynamicRepoDB2Test.java → src/test/java/us/kbase/test/narrativemethodstore/db/mongo/MongoDynamicRepoDB2Test.java

@@ -1,4 +1,4 @@
-package us.kbase.narrativemethodstore.db.mongo.test;
+package us.kbase.test.narrativemethodstore.db.mongo;
 
 import static org.hamcrest.CoreMatchers.instanceOf;
 import static org.hamcrest.CoreMatchers.is;

src/us/kbase/narrativemethodstore/db/mongo/test/MongoDynamicRepoDBTest.java → src/test/java/us/kbase/test/narrativemethodstore/db/mongo/MongoDynamicRepoDBTest.java

@@ -1,4 +1,4 @@
-package us.kbase.narrativemethodstore.db.mongo.test;
+package us.kbase.test.narrativemethodstore.db.mongo;
 
 import java.io.ByteArrayOutputStream;
 import java.io.File;

src/test/resources/us/kbase/test/narrativemethodstore/db/docker/README.md

@@ -0,0 +1,2 @@
+I'm not really sure if this file is needed anymore, but `devmin` is referenced in
+`test/data/test_repo_1/Dockerfile`