Use jitpacked jars

.github/workflows/test.yml

@@ -46,10 +46,6 @@ jobs:
           # move to parent dir of homedir to install binaries etc
           cd ..
 
-          # set up jars
-          git clone https://github.com/kbase/jars
-          export JARSDIR=$(pwd)/jars/lib/jars/
-
           # Set up mash
           wget https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar
           tar -xf mash-Linux64-v2.0.tar
@@ -66,7 +62,6 @@ jobs:
           # set up test config
           cd $HOMEDIR
           cp -n test.cfg.example test.cfg
-          sed -i "s#^test.jars.dir.*#test.jars.dir=$JARSDIR#" test.cfg
           sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg
           cat test.cfg
 

README.md

@@ -303,7 +303,8 @@ authorization source specified may be searched at the same time as namespaces wi
 * Releases
   * The master branch is the stable branch. Releases are made from the develop branch to the master
     branch.
-  * Update the version as per the semantic version rules in `src/us/kbase/assemblyhomoloy/api/Root.java`.
+  * Update the version as per the semantic version rules in
+    `src/us/kbase/assemblyhomoloy/service/api/Root.java`.
   * Tag the version in git and github.
 
 ### Running tests

build.gradle

@@ -9,8 +9,6 @@ plugins {
 	id 'org.ajoberstar.grgit' version '4.1.1'
 }
 
-// TODO NOW use jitpacked workspace client and shadow jar when available and remove jars
-
 repositories {
 	mavenCentral()
 
@@ -111,26 +109,8 @@ task buildAll {
 	dependsOn javadoc
 }
 
-def fromURL = { url, name ->
-	File file = new File("$buildDir/download/${name}.jar")
-	file.parentFile.mkdirs()
-	if (!file.exists()) {
-		new URL(url).withInputStream { downloadStream ->
-			file.withOutputStream { fileOut ->
-				fileOut << downloadStream
-			}
-		}
-	}
-	files(file.absolutePath)
-}
-
 dependencies {
 
-	implementation fromURL(
-		'https://github.com/kbase/jars/raw/master/lib/jars/kbase/workspace/WorkspaceService-0.8.0.jar',
-		'WorkspaceService-0.8.0'
-	)
-
 	implementation 'org.ini4j:ini4j:0.5.2'
 	implementation 'commons-io:commons-io:2.4'
 	implementation 'com.beust:jcommander:1.72'
@@ -143,6 +123,12 @@ dependencies {
 		exclude group: 'com.fasterxml.jackson.core'  // breaks everything if we upgrade
 		exclude group: 'javax.servlet', module: 'servlet-api'  // 2.5 vs 3.1 below
 	}
+	implementation('com.github.kbase.workspace_deluxe:workspace-client:0.15.0') {
+		exclude group: 'net.java.dev.jna' // breaks mac builds, not needed
+		exclude group: 'org.eclipse.jetty.aggregate'  // ugh, java common pollutes everything
+		exclude group: 'com.fasterxml.jackson.core'  // breaks everything if we upgrade
+		exclude group: 'javax.servlet', module: 'servlet-api'  // 2.5 vs 3.0.1 below
+	}
 	implementation 'com.github.zafarkhaja:java-semver:0.9.0'
 	implementation 'org.yaml:snakeyaml:1.18'
 	implementation 'ch.qos.logback:logback-classic:1.1.2'
@@ -159,6 +145,7 @@ dependencies {
 	implementation 'javax.xml.bind:jaxb-api:2.4.0-b180830.0359'
 
 	testImplementation "com.github.kbase:auth2:0.7.1"
+	testImplementation 'com.github.kbase.workspace_deluxe:workspace_deluxe-test-shadow-all:0.15.0'
 	testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10'
 	testImplementation 'junit:junit:4.12'
 	testImplementation('org.eclipse.jetty:jetty-servlet:9.3.11.v20160721') {

src/main/java/us/kbase/assemblyhomology/filters/KBaseAuthenticatedFilterFactory.java

@@ -170,8 +170,7 @@ public KBaseAuthenticatedFilter getFilter(
 			if (e.getMessage().contains(
 					// hacky hacky hacky
 					// ws needs error codes
-					// and we need to rewrite the auth client for auth2
-					"Login failed! Server responded with code 401 Unauthorized")) {
+					"10020 Invalid token")) {
 				throw new MinHashDistanceFilterAuthenticationException("Invalid token");
 			} else {
 				// this is annoying to test, so pass

src/main/java/us/kbase/assemblyhomology/service/api/Root.java

@@ -26,7 +26,7 @@ public class Root {
 	//TODO ZLATER ROOT add configurable contact email or link
 	//TODO ZLATER swagger
 
-	private static final String VERSION = "0.1.3";
+	private static final String VERSION = "0.1.4";
 	private static final String SERVER_NAME = "Assembly Homology service";
 
 	/** Return the root information.

src/test/java/us/kbase/test/assemblyhomology/TestCommon.java

@@ -47,8 +47,6 @@ public class TestCommon {
 	public static final String MONGOEXE = "test.mongo.exe";
 	public static final String MONGO_USE_WIRED_TIGER = "test.mongo.wired_tiger";
 
-	public static final String JARS_PATH = "test.jars.dir";
-
 	public static final String TEST_TEMP_DIR = "test.temp.dir";
 	public static final String KEEP_TEMP_DIR = "test.temp.dir.keep";
 
@@ -167,10 +165,6 @@ public static Path getMongoExe() {
 		return Paths.get(getTestProperty(MONGOEXE)).toAbsolutePath().normalize();
 	}
 
-	public static Path getJarsDir() {
-		return Paths.get(getTestProperty(JARS_PATH)).toAbsolutePath().normalize();
-	}
-
 	public static Path getTempDir() {
 		return Paths.get(getTestProperty(TEST_TEMP_DIR)).toAbsolutePath().normalize();
 	}

src/test/java/us/kbase/test/assemblyhomology/integration/ServiceIntegrationTest.java

@@ -74,11 +74,11 @@
 import us.kbase.test.assemblyhomology.data.TestDataManager;
 import us.kbase.test.assemblyhomology.service.api.RootTest;
 import us.kbase.test.auth2.authcontroller.AuthController;
+import us.kbase.test.workspace.controllers.workspace.WorkspaceController;
 import us.kbase.workspace.CreateWorkspaceParams;
 import us.kbase.workspace.SetPermissionsParams;
 import us.kbase.workspace.WorkspaceClient;
 import us.kbase.test.assemblyhomology.TestCommon;
-import us.kbase.test.assemblyhomology.controllers.workspace.WorkspaceController;
 
 public class ServiceIntegrationTest {
 
@@ -195,9 +195,9 @@ public static void beforeClass() throws Exception {
 
 		// set up Workspace
 		WS = new WorkspaceController(
-				TestCommon.getJarsDir(),
 				"localhost:" + MANAGER.mongo.getServerPort(),
 				"AssemblyHomologyServiceIntegTestWSDB",
+				"AssemblyHomologyServiceIntegTestWSDB_types",
 				"fakeadmin",
 				authURL,
 				TEMP_DIR);
@@ -485,8 +485,6 @@ public void searchNamespace() throws Exception {
 				Files.newInputStream(TEMP_DIR.resolve(QUERY_K31_S1500)),
 				MediaType.APPLICATION_OCTET_STREAM));
 
-		assertThat("incorrect response code", res.getStatus(), is(200));
-
 		@SuppressWarnings("unchecked")
 		final Map<String, Object> response = res.readEntity(Map.class);
 
@@ -515,6 +513,7 @@ public void searchNamespace() throws Exception {
 				);
 
 		assertThat("incorrect response", response, is(expected));
+		assertThat("incorrect response code", res.getStatus(), is(200));
 	}
 
 	@Test

src/test/java/us/kbase/test/assemblyhomology/service/api/RootTest.java

@@ -17,7 +17,7 @@
 
 public class RootTest {
 
-	public static final String SERVER_VER = "0.1.3";
+	public static final String SERVER_VER = "0.1.4";
 	private static final String GIT_ERR = 
 			"Missing git commit file gitcommit, should be in us.kbase.assemblyhomology";
 

test.cfg.example

@@ -6,9 +6,6 @@
 # path to the mongodb executable to use for the tests.
 test.mongo.exe=/path/to/mongodbexecutable
 
-# path to the KBase jars directory, e.g. [path to parent folder]/jars/lib/jars
-test.jars.dir=/path/to/jars/dir
-
 # true to use wired tiger, anything else for false.
 test.mongo.wired_tiger=false