Merge pull request #157 from kbase/sdkdev

Use NMS & catalog Jitpack jars

Author: MrCreosote

build.gradle

@@ -167,19 +167,6 @@ jacocoTestReport {
 		xml.required = true
 		csv.required = true
 	}
-	
-	// Exclude specific directories or files from coverage
-	afterEvaluate {
-		classDirectories.setFrom(
-			files(classDirectories.files.collect {
-				fileTree(dir: it, exclude: [
-					'**/common/service/**',
-					'**/catalog/**',
-					'**/narrativemethodstore/**',
-				])
-			})
-		)
-	}
 }
 
 // TODO BUILD the other script tasks could possibly be made simpler with some of the 
@@ -309,16 +296,23 @@ dependencies {
 	implementation('com.github.kbase:auth2_client_java:0.5.0') {
 		exclude group: 'com.fasterxml.jackson.core'  // don't upgrade yet, breaks tests
 	}
+	implementation('com.github.kbase:catalog:2.3.1') {
+		exclude group: 'com.github.kbase', module: 'java_common'
+		exclude group: 'com.fasterxml.jackson.core'  // don't upgrade yet, breaks tests
+	}
 	implementation('com.github.kbase:java_common:0.3.1') {
 		exclude group: 'com.fasterxml.jackson.core'  // don't upgrade yet, breaks tests
 		exclude group: 'net.java.dev.jna' // don't include in runtime path
+		exclude group: 'org.eclipse.jetty.aggregate' // don't include in runtime path
+		exclude group: 'org.syslog4j', module: 'syslog4j'
 	}
 	implementation('com.github.kbase:java_kidl:0.2.0')
-	// TODO DEPS see if this can be removed after switching to the python callback server
-	//           Provenance classes are used in various callback server related classes and tests
-	implementation('com.github.kbase.workspace_deluxe:workspace-client:0.15.0') {
+	implementation('com.github.kbase:narrative_method_store:v0.3.13') {
+		exclude group: 'com.github.kbase', module: 'java_common'
 		exclude group: 'com.fasterxml.jackson.core'  // don't upgrade yet, breaks tests
-		exclude group: 'net.java.dev.jna' // don't include in runtime path
+		// TODO DEPS fix these in NMS
+		exclude group: 'org.mongodb'
+		exclude group: 'org.eclipse.jetty.aggregate' // don't include in runtime path
 	}
 	implementation('com.fasterxml.jackson.core:jackson-annotations:2.2.3')
 	implementation('com.fasterxml.jackson.core:jackson-databind:2.2.3')
@@ -329,42 +323,41 @@ dependencies {
 	}
 	implementation('commons-io:commons-io:2.4')
 	implementation('info.picocli:picocli:4.7.7')
+	// TODO DEPS the annotation api is needed for
+	//           a couple of SDK compiled classes in mobu/runner that should be factored out
+	implementation('javax.annotation:javax.annotation-api:1.3.2')
 	implementation('org.apache.commons:commons-lang3:3.1')
 	implementation('org.apache.velocity:velocity:1.7')
 	implementation('org.ini4j:ini4j:0.5.2')
 	implementation('com.sun.codemodel:codemodel:2.4.1')
 	implementation('org.yaml:snakeyaml:1.11')
 	implementation('com.github.zafarkhaja:java-semver:0.10.2')
 
-	// TODO DEPS the deps below are required due to a) the callback server code, b)
-	//           tests that mock service wizard and the callback service and
-	//           c) java modules created by tests. See if they can be
-	//           moved to a test implementation if we swap the callback service for the
-	//           python docker image
-	implementation('ch.qos.logback:logback-classic:1.1.2')
-	implementation('org.slf4j:slf4j-api:1.7.7')
-	// TODO DEPS the annotation api is also needed for
-	//           a couple of SDK compiled classes in mobu/runner that should be factored out
-	implementation('javax.annotation:javax.annotation-api:1.3.2')
-	implementation('joda-time:joda-time:2.2')
-	// this is OOOOOOLD. But that probably means updating java_common
-	implementation('org.eclipse.jetty.aggregate:jetty-all:7.0.0.v20091005')
-	// TODO DEPS Need to rework the java common logger to not use syslog4j at all since it's
-	// abandonware and has a ton of CVEs, even in the newer versions.
-	// Note that the java SDK modules use syslog4j, so we'll need to figure something out
-	// there. I doubt any of the apps actually use the logging code that triggers it though
-	implementation('org.syslog4j:syslog4j:0.9.46')
 
+	testImplementation('ch.qos.logback:logback-classic:1.1.2')
 	testImplementation ('com.github.kbase:java_test_utilities:0.1.0') {
 		exclude group: 'com.fasterxml.jackson.core'  // don't upgrade yet, breaks tests
 		exclude group: 'junit', module: 'junit'
 	}
+	testImplementation('com.github.kbase.workspace_deluxe:workspace-client:0.15.0') {
+		exclude group: 'com.fasterxml.jackson.core'  // don't upgrade yet, breaks tests
+		exclude group: 'net.java.dev.jna' // don't include in runtime path
+	}
+	testImplementation('joda-time:joda-time:2.2')
 	// needed for syslog4j. Used in java test modules and JsonServerServlet subclasses in tests
 	// but not in SDK code proper.
 	testImplementation('net.java.dev.jna:jna:3.4.0')
 	testImplementation("nl.jqno.equalsverifier:equalsverifier:4.0.7")
+	// this is OOOOOOLD. But that probably means updating java_common
+	testImplementation('org.eclipse.jetty.aggregate:jetty-all:7.0.0.v20091005')
 	testImplementation('org.hamcrest:hamcrest:3.0')
 	testImplementation('org.junit.jupiter:junit-jupiter:5.13.1')
+	testImplementation('org.slf4j:slf4j-api:1.7.7')
+	// TODO DEPS Need to rework the java common logger to not use syslog4j at all since it's
+	// abandonware and has a ton of CVEs, even in the newer versions.
+	// Note that the java SDK modules use syslog4j, so we'll need to figure something out
+	// there. I doubt any of the apps actually use the logging code that triggers it though
+	testImplementation('org.syslog4j:syslog4j:0.9.46')
 
 	// isolate the sdk generated code dependencies from the standard dependencies