diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..097f9f9
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,9 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# Linux start script should use lf
+/gradlew        text eol=lf
+
+# These are Windows script files and should use crlf
+*.bat           text eol=crlf
+
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f7ef41b..5e6bfab 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -25,10 +25,10 @@ jobs:
           # the current production setup
           - java: '8'
             mongo: 'mongodb-linux-x86_64-3.6.13'
-            ant_test: 'test'
+            gradle_test: 'test'
           - java: '11'
             mongo: 'mongodb-linux-x86_64-3.6.23'
-            ant_test: 'test'
+            gradle_test: 'test'
     steps:
       - uses: actions/checkout@v3
 
@@ -75,7 +75,7 @@ jobs:
         run: |
           PATH=$PATH:$MASH_PATH
           echo $PATH
-          ant ${{matrix.ant_test}}
+          ./gradlew ${{matrix.gradle_test}}
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
diff --git a/Dockerfile b/Dockerfile
index 71fbb1b..fe612e4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,10 +1,22 @@
 FROM kbase/sdkbase2 as build
-RUN cd / && git clone https://github.com/kbase/jars
 
+WORKDIR /tmp/ah
 
-ADD . /src
-RUN cd /src && ant build
-RUN find /src
+# dependencies take a while to D/L, so D/L & cache before the build so code changes don't cause
+# a new D/L
+# can't glob *gradle because of the .gradle dir
+COPY build.gradle gradlew settings.gradle /tmp/ah/
+COPY gradle/ /tmp/ah/gradle/
+RUN ./gradlew dependencies
+
+# Now build the code
+COPY deployment/ /tmp/ah/deployment/
+COPY jettybase/ /tmp/ah/jettybase/
+COPY src /tmp/ah/src/
+COPY war /tmp/ah/war/
+# for the git commit
+COPY .git /tmp/ah/.git/
+RUN ./gradlew war
 
 
 FROM kbase/kb_jre:latest
@@ -14,10 +26,9 @@ ARG BUILD_DATE
 ARG VCS_REF
 ARG BRANCH=develop
 
-COPY --from=build /src/deployment/ /kb/deployment/
-COPY --from=build /src/jettybase/ /kb/deployment/jettybase/
-COPY --from=build /src/dist/ /src/dist/
-COPY --from=build /src/assembly_homology /kb/deployment/bin/
+COPY --from=build /tmp/ah/deployment/ /kb/deployment/
+COPY --from=build /tmp/ah/jettybase/ /kb/deployment/jettybase/
+COPY --from=build /tmp/ah/build/libs/AssemblyHomologyService.war /kb/deployment/jettybase/webapps/ROOT.war
 
 # The BUILD_DATE value seem to bust the docker cache when the timestamp changes, move to
 # the end
@@ -33,6 +44,9 @@ ENV ASSEMBLY_HOMOLOGY_CONFIG=/kb/deployment/conf/deployment.cfg
 ENV PATH=/bin:/usr/bin:/kb/deployment/bin
 ENV JETTY_HOME=/usr/local/jetty
 
+# TODO BUILD update to no longer use dockerize and take env vars (e.g. like Collections).
+# TODO BUILD Use subsections in the ini file / switch to TOML
+
 RUN wget https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar && \
     tar xf mash-Linux64-v2.0.tar && \
     cp mash-Linux64-v2.0/mash /usr/bin/mash
diff --git a/README.md b/README.md
index fbe56b6..9f18f2b 100644
--- a/README.md
+++ b/README.md
@@ -4,8 +4,6 @@ This repo contains the KBase / JGI Assembly Homology Service (AHS). The service
 assembly matching based on implementations of the
 [MinHash algorithm](https://ieeexplore.ieee.org/abstract/document/666900/?reload=tru).
 
-Build status (master):
-[![Build Status](https://travis-ci.org/jgi-kbase/AssemblyHomologyService.svg?branch=master)](https://travis-ci.org/jgi-kbase/AssemblyHomologyService)
 [![codecov](https://codecov.io/gh/jgi-kbase/AssemblyHomologyService/branch/master/graph/badge.svg)](https://codecov.io/gh/jgi-kbase/AssemblyHomologyService)
 
 ## Usage
@@ -33,21 +31,20 @@ is supported. Mash is configured to never return sequences with a distance great
 ## Requirements
 
 Java 8 (OpenJDK OK)  
-Apache Ant (http://ant.apache.org/)  
 MongoDB 2.6+ (https://www.mongodb.com/)  
 Jetty 9.3+ (http://www.eclipse.org/jetty/download.html)
     (see jetty-config.md for version used for testing)  
 This repo (git clone https://github.com/jgi-kbase/AssemblyHomologyService)  
-The jars repo (git clone https://github.com/kbase/jars)  
-The two repos above need to be in the same parent folder.
 
 ## Build
 
 ```
 cd [assembly homology repo directory]
-ant build
+./gradlew buildAll
 ```
 
+Build artifacts reside in the `build` directory.
+
 ## Load data
 
 These instructions assume
@@ -230,7 +227,13 @@ processing and either discard or pass on all distances to the collector.
 ensure `mash` is available on the system path  
 start mongodb  
 cd into the assembly homology repo  
-`ant build`  
+
+```
+./gradlew buildAll
+mkdir jettybase/webapps
+cp build/libs/AssemblyHomologyService.war jettybase/webapps/ROOT.war
+```
+
 copy `deploy.cfg.example` to `deploy.cfg` and fill in appropriately  
 `export ASSEMBLY_HOMOLOGY_CONFIG=<path to deploy.cfg>`  
 OR  
@@ -306,8 +309,7 @@ authorization source specified may be searched at the same time as namespaces wi
 ### Running tests
 
 * Copy `test.cfg.example` to `test.cfg` and fill in the values appropriately.
-  * If it works as is start buying lottery tickets immediately.
-* `ant test`
+* `./gradlew test`
 
 ### UI
 
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 7bc67ce..0b4943a 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,5 +1,10 @@
 # Assembly Homology Service release notes
 
+## 0.1.4
+
+* Switched the build system from Ant to Gradle. As such, all build artifacts, including the
+  `assembly_homology` script, are now found in the `build` directory.
+
 ## 0.1.3
 
 * Update the Java Mongo client to 3.10.1. This supports the latest Mongo version, 4.0.
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 0000000..f195c58
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,200 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+	id 'java'
+	id 'war'
+	id 'jacoco'
+	id 'org.ajoberstar.grgit' version '4.1.1'
+}
+
+// TODO NOW switch to std gradle layout
+// TODO NOW use jitpacked workspace client and shadow jar when available and remove jars
+
+repositories {
+	mavenCentral()
+	
+	maven {
+		name = "Clojars"
+		url = "https://repo.clojars.org/"
+	}
+	maven {
+		name = "JitPack" 
+		url = 'https://jitpack.io'
+	}
+}
+task buildGitCommitFile {
+	doLast {
+		def commitId = grgit.head().id
+		// is there a variable for builddir/classes/java/main?
+		file("$buildDir/classes/java/main/us/kbase/assemblyhomology/gitcommit").text = commitId
+	}
+}
+
+compileJava {
+	// TODO BUILD remove when we no longer support java 8, use `options.release = 11` if needed
+	java.sourceCompatibility = JavaVersion.VERSION_1_8
+	java.targetCompatibility = JavaVersion.VERSION_1_8
+	finalizedBy buildGitCommitFile
+}
+
+test {
+	/* 
+	 * TODO TEST Figure out why tests fail without this and remove. Might have something to do
+	 * with the stfuLoggers() call in many of the tests, might kill logging for tests that
+	 * require it
+	 * Although it seems to make Mongo start up correctly as well which is odd
+	 */
+	forkEvery = 1
+	/*
+	  * TODO TEST split tests into mongo wrapper tests & all other tests (incl. integration).
+	  * Set up GHA to run the non-mongo tests with a single version of mongo and run the
+	  * mongo tests with matrixed mongo versions. Combine coverage at the end somehow
+	*/
+	systemProperty "ASSEMHOMOL_TEST_CONFIG", "./test.cfg"
+	testLogging {
+		exceptionFormat = 'full'
+		showStandardStreams = true
+	}
+	finalizedBy jacocoTestReport
+}
+
+// TODO TEST add a test that starts the server in a docker container and checks some simple cmds
+
+jacocoTestReport {
+	reports {
+		xml.required = true
+		csv.required = true
+	}
+}
+
+javadoc {
+	options {
+		// I don't know why this isn't working, but it's not worth spending time on right now
+		links "https://docs.oracle.com/javase/8/docs/api/"
+	}
+}
+
+war {
+	webXml = file('war/web.xml')
+}
+
+configurations {
+	// can't directly access testImplementation, so extend and access
+	testimpl.extendsFrom testImplementation
+}
+
+task generateCLIScript {
+	dependsOn compileJava
+	doLast {
+		def dependencies = configurations.runtimeClasspath.collect { File file ->
+			file.absolutePath
+		}
+	
+		def classpath = dependencies.join(':')
+	
+		def scriptContent = """#!/bin/sh
+
+CLASSPATH=$classpath
+
+java -cp build/classes/java/main:\$CLASSPATH us.kbase.assemblyhomology.cli.AssemblyHomologyCLI \$@
+"""
+
+		file("$buildDir/assembly_homology").text = scriptContent
+		file("$buildDir/assembly_homology").setExecutable(true)
+	}
+}
+
+task buildAll {
+	dependsOn generateCLIScript
+	dependsOn war
+	dependsOn javadoc
+}
+
+sourceSets {
+	main {
+		java {
+			srcDirs = ["src"]
+			exclude '**/test/**'
+		}
+	}
+	test {
+		java {
+			srcDirs = ["src"]
+			include '**/test/**'
+		}
+		resources {
+			srcDirs = ["src"]
+			include "**/*.msh"
+			include "**/*.txt"
+			include "**/wsjars"
+		}
+	}
+}
+
+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'
+	implementation 'org.mongodb:mongo-java-driver:3.10.1'
+	implementation 'com.google.guava:guava:18.0'
+	implementation "com.github.kbase:auth2_client_java:0.5.0"
+	implementation('com.github.kbase:java_common:0.3.0') {
+		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 3.1 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'
+	implementation 'org.slf4j:slf4j-api:1.7.25'
+	// 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.
+	implementation "org.syslog4j:syslog4j:0.9.46"
+	implementation 'com.fasterxml.jackson.core:jackson-annotations:2.5.4'
+	implementation 'com.fasterxml.jackson.core:jackson-databind:2.5.4'
+	implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4'
+	implementation 'org.glassfish.jersey.containers:jersey-container-servlet:2.23.2'
+	implementation 'org.glassfish.jersey.media:jersey-media-json-jackson:2.23.2'
+	implementation 'javax.servlet:javax.servlet-api:3.0.1'
+	implementation 'javax.xml.bind:jaxb-api:2.4.0-b180830.0359'
+	
+	testImplementation "com.github.kbase:auth2:0.7.1"
+	testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10'
+	testImplementation 'junit:junit:4.12'
+	testImplementation('org.eclipse.jetty:jetty-servlet:9.3.11.v20160721') {
+		exclude group: "javax.servlet", module: "javax.servlet-api" // upgrading breaks tests
+	}
+	testImplementation 'org.mockito:mockito-core:3.0.0'
+	testImplementation 'org.apache.commons:commons-lang3:3.5'
+	testImplementation('com.github.kbase:java_test_utilities:0.1.0') {
+		exclude group: 'com.fasterxml.jackson.core'  // upgrading breaks stuff
+	}
+}
+
+task showTestClassPath {
+	doLast {
+		configurations.testimpl.each { println it }
+	}
+}
diff --git a/build.xml b/build.xml
deleted file mode 100644
index f803fdf..0000000
--- a/build.xml
+++ /dev/null
@@ -1,350 +0,0 @@
-<project name="KBase / JGI Assembly Homology Service" default="test" basedir="."
-  xmlns:jacoco="antlib:org.jacoco.ant">
-
-  <description>
-      Build file for the joint KBase / JGI Assembly Homology Service 
-  </description>
-	
-  <!-- TODO ZLATER BUILD switch to gradle or at least ivy -->
-
-  <!-- set global properties for this build -->
-  <property name="package" value="KBase / JGI Assembly Homology Service"/>
-  <property name="src" location="src"/>
-  <property name="lib" location="lib"/>
-  <property name="dist" location="dist"/>
-  <property name="jardir" location="../jars/lib/jars/"/>
-  <property name="classes" location="classes"/>
-  <property name="doc" location="docs/javadoc"/>
-  <property name="testcfg" location="./test.cfg"/>
-  <property name="testjar.file" value="AssemblyHomologyTest.jar"/>
-  <property name="jar.file" value="AssemblyHomology.jar"/>
-  <property name="war.file" value="AssemblyHomology.war"/>
-  <property name="war.dir" value="war"/>
-  <property name="test.dir" location="${src}/us/kbase/test"/>
-  <property name="test.reports.dir" location="test-reports"/>
-
-  <fileset dir="${jardir}" id="lib">
-    <include name="apache_commons/commons-io-2.4.jar"/>
-    <include name="google/guava-18.0.jar"/>
-    <include name="ini4j/ini4j-0.5.2.jar"/>
-    <include name="jcommander/jcommander-1.72.jar"/>
-    <include name="mongo/mongo-java-driver-3.10.1.jar"/>
-    <include name="snakeyaml/snakeyaml-1.18.jar"/>
-    <include name="kbase/workspace/WorkspaceClient-0.8.0.jar"/>
-    <include name="kbase/auth/kbase-auth-0.4.4.jar"/>
-    <include name="jsemver/java-semver-0.9.0.jar"/>
-  </fileset>
-
-  <fileset dir="${jardir}" id="logging">
-    <include name="kbase/common/kbase-common-0.0.24.jar"/>
-    <include name="logback/logback-core-1.1.2.jar"/>
-    <include name="logback/logback-classic-1.1.2.jar"/>
-    <include name="slf4j/slf4j-api-1.7.25.jar"/>
-    <include name="syslog4j/syslog4j-0.9.46.jar"/>
-    <include name="jna/jna-3.4.0.jar"/>
-  </fileset>
-	
-  <fileset dir="${jardir}" id="jackson">
-    <include name="jackson/jackson-annotations-2.5.4.jar"/>
-    <include name="jackson/jackson-core-2.5.4.jar"/>
-    <include name="jackson/jackson-databind-2.5.4.jar"/>
-    <include name="jackson/jackson-jaxrs-base-2.5.4.jar"/>
-    <include name="jackson/jackson-jaxrs-json-provider-2.5.4.jar"/>
-    <include name="jackson/jackson-module-jaxb-annotations-2.5.4.jar"/>
-  </fileset>
-	
-  <fileset dir="${jardir}" id="jersey">
-    <include name="jersey/entity-filtering/jersey-entity-filtering-2.23.2.jar"/>
-    <include name="jersey/entity-filtering/jersey-media-json-jackson-2.23.2.jar"/>
-    <include name="jersey/jersey-client-2.23.2.jar"/>
-    <include name="jersey/jersey-common-2.23.2.jar"/>
-    <include name="jersey/jersey-container-servlet-2.23.2.jar"/>
-    <include name="jersey/jersey-container-servlet-core-2.23.2.jar"/>
-    <include name="jersey/jersey-guava-2.23.2.jar"/>
-    <include name="jersey/jersey-media-jaxb-2.23.2.jar"/>
-    <include name="jersey/jersey-server-2.23.2.jar"/>
-  </fileset>
-
-  <fileset dir="${jardir}" id="jerseydeps">
-    <include name="annotation/javax.annotation-api-1.2.jar"/>
-    <include name="asm/asm-debug-all-5.0.4.jar"/>
-    <include name="inject/javax.inject-2.5.0-b05.jar"/>
-    <include name="javassist/javassist-3.20.0-GA.jar"/>
-    <include name="jaxb/jaxb-api-2.2.7.jar"/>
-    <include name="jaxrs/javax.ws.rs-api-2.0.1.jar"/>
-    <include name="osgi/org.osgi.core-4.2.0.jar"/>
-    <include name="persistence/persistence-api-1.0.jar"/>
-    <include name="servlet/javax.servlet-api-3.0.1.jar"/>
-    <include name="validationapi/validation-api-1.1.0.Final.jar"/>
-    <include name="activation/activation-1.1.jar"/>
-  </fileset>
-
-  <fileset dir="${jardir}" id="jerseydep_hk2">
-    <include name="hk2/aopalliance-repackaged-2.5.0-b05.jar"/>
-    <include name="hk2/hk2-api-2.5.0-b05.jar"/>
-    <include name="hk2/hk2-locator-2.5.0-b05.jar"/>
-    <include name="hk2/hk2-utils-2.5.0-b05.jar"/>
-    <include name="hk2/osgi-resource-locator-1.0.1.jar"/>
-  </fileset>
-	
-  <fileset dir="${jardir}" id="testlibs">
-    <include name="equalsverifier/equalsverifier-3.1.10.jar"/>
-    <include name="junit/junit-4.12.jar"/>
-    <include name="hamcrest/hamcrest-core-1.3.jar"/>
-    <include name="jetty/jetty-all-9.3.11.v20160721-uber.jar"/>
-    <include name="apache_commons/commons-lang3-3.5.jar"/>
-    <include name="kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar"/>
-    <!-- mockito and dependencies -->
-    <include name="mockito/mockito-core-3.0.0.jar"/>
-    <include name="bytebuddy/byte-buddy-1.9.10.jar"/>
-    <include name="bytebuddy/byte-buddy-agent-1.9.10.jar"/>
-    <include name="objenesis/objenesis-2.6.jar"/>
-  </fileset>
-	
-  <union id="applicationjars">
-    <fileset refid="jerseydeps"/>
-    <fileset refid="jerseydep_hk2"/>
-    <fileset refid="jackson"/>
-    <fileset refid="jersey"/>
-    <fileset refid="lib"/>
-    <fileset refid="logging"/>
-  </union>
-
-  <path id="compile.classpath">
-    <union refid="applicationjars"/>
-    <fileset refid="testlibs"/>
-  </path>
-
-  <path id="test.classpath">
-    <path refid="compile.classpath"/>
-    <fileset file="${dist}/${jar.file}"/>
-    <fileset file="${dist}/${testjar.file}"/>
-  </path>
-	
-  <target name="build" depends="compile,buildwar,script,javadoc"
-    description="build everything"/>
-
-  <target name="init" description="make directories">
-    <!-- Create the output directory structure-->
-    <mkdir dir="${classes}"/>
-    <mkdir dir="${dist}"/>
-    <mkdir dir="${test.reports.dir}"/>
-    <mkdir dir="${test.reports.dir}/html"/>
-  </target>
-
-  <target name="compile" depends="init" description="compile the source">
-    <!-- Compile class files-->
-    <javac srcdir="${src}"
-           destdir="${classes}"
-           includeantruntime="false"
-           debug="true"
-           classpathref="compile.classpath"
-           target="1.8"
-           source="1.8">
-      <compilerarg line="-encoding utf-8"/>
-    </javac>
-    <!-- Copy resource files-->
-    <copy todir="${classes}">
-      <fileset dir="${src}">
-        <patternset>
-          <include name="**/*.msh"/>
-          <include name="**/*.txt"/>
-          <include name="**/wsjars"/>
-        </patternset>
-      </fileset>
-    </copy>
-    <!-- add git commit to file -->
-    <exec executable="git" output="${classes}/us/kbase/assemblyhomology/gitcommit">
-      <arg line="rev-parse HEAD"/>
-    </exec>
-    <!-- Make main jar file-->
-    <jar destfile="${dist}/${jar.file}"
-         basedir="${classes}"
-         includes="us/kbase/assemblyhomology/**"
-    />
-    <!-- Make test jar file-->
-    <jar destfile="${dist}/${testjar.file}"
-         basedir="${classes}"
-         includes="us/kbase/test/**"
-    />
-  </target>
-
-  <target name="buildwar" depends="compile" description="build the WAR file">
-    <!-- make the war file for the server-->
-    <mkdir dir="${war.dir}/lib"/>
-    <copy todir="${war.dir}/lib/" flatten="true">
-      <union refid="applicationjars"/>
-    </copy>
-    <war destfile="${dist}/${war.file}" webxml="${war.dir}/web.xml">
-      <classes dir="${classes}" includes="us/kbase/assemblyhomology/**"/>
-      <lib dir="${war.dir}/lib/"/>
-    </war>
-    <!-- Remove uncompressed class files and libs-->
-    <delete dir="${war.dir}/lib"/>
-    <!-- copy war to jettybase -->
-    <copy tofile="./jettybase/webapps/ROOT.war" file="${dist}/${war.file}" />
-  </target>
-
-  <target name="docker_image" depends="buildwar" description="build the docker image">
-    <!-- make the docker image that for auth2 -->
-    <exec executable="./build/build_docker_image.sh">
-    </exec>
-
-  </target>
-
-  <target name="javadoc" description="build javadocs">
-    <javadoc access="protected"
-             author="false"
-             classpathref="compile.classpath"
-             destdir="${doc}"
-             sourcepath="${src}"
-             excludepackagenames="us.kbase.test.*"
-             nodeprecated="false"
-             nodeprecatedlist="false"
-             noindex="false"
-             nonavbar="false"
-             notree="false"
-             source="1.8"
-             splitindex="true"
-             use="true"
-             version="true">
-      <link href="https://docs.oracle.com/javase/8/docs/api/"/>
-      <link href="http://api.mongodb.com/java/3.3/"/>
-      <link href="https://google.github.io/guava/releases/18.0/api/docs/"/>
-    </javadoc>
-  </target>
-
-  <path id="jacoco.classpath">
-    <fileset dir="${jardir}">
-        <include name="jacoco/org.jacoco.ant-0.8.4.jar"/>
-        <include name="jacoco/org.jacoco.core-0.8.4.jar"/>
-        <include name="jacoco/org.jacoco.report-0.8.4.jar"/>
-        <include name="jacoco/org.jacoco.agent-0.8.4.jar"/>
-        <include name="asm/asm-7.1.jar"/>
-        <include name="asm/asm-commons-7.1.jar"/>
-        <include name="asm/asm-analysis-7.1.jar"/>
-        <include name="asm/asm-tree-7.1.jar"/>
-    </fileset>
-  </path>
-
-  <taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml"
-    classpathref="jacoco.classpath"/>
-	
-  <target name="test"
-          depends="test_no_mongo_storage,test_mongo_storage"
-          description="run all tests and generate test report">
-    <delete file="${test.reports.dir}/merged_jacoco.exec"/>
-    <jacoco:merge destfile="${test.reports.dir}/merged_jacoco.exec">
-      <fileset dir="${test.reports.dir}" includes="*.exec"/>
-    </jacoco:merge>
-    <jacoco:report>
-      <executiondata>
-        <file file="${test.reports.dir}/merged_jacoco.exec"/>
-      </executiondata>
-      <structure name="Assembly Homology Unit Tests">
-        <classfiles>
-          <fileset dir="${classes}">
-            <exclude name="**/test/**"/>
-          </fileset>
-        </classfiles>
-        <sourcefiles encoding="UTF-8">
-          <fileset dir="${src}">
-            <exclude name="**/test/**"/>
-          </fileset>
-        </sourcefiles>
-      </structure>
-      <html destdir="${test.reports.dir}/html"/>
-      <csv destfile="${test.reports.dir}/coverage-report.csv"/>
-      <xml destfile="${test.reports.dir}/coverage-report.xml"/>
-    </jacoco:report>
-  </target>
-	
-  <target name="test_no_mongo_storage"
-          depends="compile"
-          description="run tests without the MongoStorage* tests">
-    <echo message="starting ${package} tests"/>
-    <delete file="${test.reports.dir}/no_mongo_storage_jacoco.exec"/>
-    <jacoco:coverage destfile="${test.reports.dir}/no_mongo_storage_jacoco.exec"
-        excludes="org/*:junit/*">
-      <junit printsummary="yes" failureproperty="test.failed" fork="yes">
-        <classpath refid="test.classpath"/>
-        <formatter type="plain" usefile="false" />
-        <sysproperty key="ASSEMHOMOL_TEST_CONFIG" value="${testcfg}"/>
-        <test name="us.kbase.test.assemblyhomology.config.AssemblyHomologyConfigTest"/>
-        <test name="us.kbase.test.assemblyhomology.config.FilterConfigurationTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.AssemblyHomologyTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.FilterIDTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.DataSourceIDTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.LoadIDTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.NameTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.NamespaceTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.NamespaceIDTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.NamespaceViewTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.SequenceMatchesTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.SequenceMetadataTest"/>
-        <test name="us.kbase.test.assemblyhomology.core.TokenTest"/>
-        <test name="us.kbase.test.assemblyhomology.filters.KBaseAuthenticatedFilterTest"/>
-        <test name="us.kbase.test.assemblyhomology.integration.CLIIntegrationTest"/>
-        <test name="us.kbase.test.assemblyhomology.integration.ServiceIntegrationTest"/>
-        <test name="us.kbase.test.assemblyhomology.load.LoaderTest"/>
-        <test name="us.kbase.test.assemblyhomology.load.NamespaceLoadInfoTest"/>
-        <test name="us.kbase.test.assemblyhomology.load.ParseHelpersTest"/>
-        <test name="us.kbase.test.assemblyhomology.load.SeqMetaLoadInfoTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.DefaultDistanceCollectorTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.DefaultDistanceFilterTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.MinHashDBLocationTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.MinHashDistanceTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.MinHashImplementationInformationTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.MinHashImplementationNameTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.MinHashParametersTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.MinHashSketchDatabaseTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.MinHashSketchDBNameTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.mash.MashFactoryTest"/>
-        <test name="us.kbase.test.assemblyhomology.minhash.mash.MashTest"/>
-        <test name="us.kbase.test.assemblyhomology.service.LoggingFilterTest"/>
-        <test name="us.kbase.test.assemblyhomology.service.api.NamespacesTest"/>
-        <test name="us.kbase.test.assemblyhomology.service.api.RootTest"/>
-        <test name="us.kbase.test.assemblyhomology.service.exceptions.ErrorMessageTest"/>
-        <test name="us.kbase.test.assemblyhomology.service.exceptions.ExceptionHandlerTest"/>
-        <test name="us.kbase.test.assemblyhomology.util.CappedTreeSetTest"/>
-        <test name="us.kbase.test.assemblyhomology.util.PathRestreamableTest"/>
-        <test name="us.kbase.test.assemblyhomology.util.UtilTest"/>
-      </junit>
-    </jacoco:coverage>
-    <fail message="Test failure detected, check test results." if="test.failed" />
-  </target>
-
-  <target name="test_mongo_storage"
-          depends="compile"
-          description="run only the MongoStorage* tests">
-    <echo message="starting ${package} tests"/>
-    <delete file="${test.reports.dir}/mongo_storage_jacoco.exec"/>
-    <jacoco:coverage destfile="${test.reports.dir}/mongo_storage_jacoco.exec"
-        excludes="org/*:junit/*">
-      <junit failureproperty="test.failed" fork="yes">
-        <classpath refid="test.classpath"/>
-        <formatter type="plain" usefile="false" />
-        <sysproperty key="ASSEMHOMOL_TEST_CONFIG" value="${testcfg}"/>
-        <test name="us.kbase.test.assemblyhomology.storage.MongoAssemblyHomologyStorageStartupTest"/>
-        <test name="us.kbase.test.assemblyhomology.storage.MongoAssemblyHomologyStorageOpsTest"/>
-      </junit>
-    </jacoco:coverage>
-    <fail message="Test failure detected, check test results." if="test.failed" />
-  </target>
-
-  <target name="script" depends="compile" description="create cli script">
-    <pathconvert targetos="unix" property="lib.classpath" refid="applicationjars"/>
-    <echo file="./assembly_homology">#!/bin/sh
-java -cp ${dist}/${jar.file}:${lib.classpath} us.kbase.assemblyhomology.cli.AssemblyHomologyCLI $@
-    </echo>
-    <chmod file="./assembly_homology" perm="a+x"/>
-  </target>
-	
-  <target name="clean" description="clean up" >
-    <!-- Clean up internal temporary files and folders-->
-    <delete dir="${classes}"/>
-    <delete dir="${test.reports.dir}"/>
-    <delete dir="${dist}"/>
-  </target>
-</project>
-
diff --git a/docker-compose.yml b/docker-compose.yml
index 2063d41..3e7125f 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -5,20 +5,24 @@ version: "3.1"
 # that is started up and polled
 services:
   assembly_homology:
-    image: kbase/assembly_homology:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
     ports:
       - "8080:8080"
     environment:
-      - ASSEMBLY_HOMOLOGY_CONFIG=/kb/deployment/conf/deployment.cfg
+      mongo_host: "mongo:27017"
     command:
       - "-wait"
-      - "tcp://ci-mongo:27017"
-      - "-wait"
-      - "tcp://mongoinit:8080"
+      - "tcp://mongo:27017"
       - "-timeout"
       - "120s"
       - "-template"
       - "/kb/deployment/conf/.templates/deployment.cfg.templ:/kb/deployment/conf/deployment.cfg"
+      - "java"
+      - "-Djetty.home=/usr/local/jetty"
+      - "-jar"
+      - "/usr/local/jetty/start.jar"
       # If you needed to pass in context for template evaluation you would put something like
       # these lines that tell dockerize to hit github for an INI style file for the context
     # - "-env"
@@ -34,22 +38,10 @@ services:
       # If your server is using self-signed certs, or otherwise problematic for cert validation
       # you can add the following flag:
     # - "-validateCert=false"
-    depends_on: ["ci-mongo", "mongoinit"]
+    depends_on: ["mongo"]
 
-  mongoinit:
-    image: kbase/db_initialize:latest
-    entrypoint:
-      - "/kb/deployment/bin/dockerize.sh"
-      - "-wait"
-      - "tcp://ci-mongo:27017"
-      - "-timeout"
-      - "120s"
-    depends_on: [ "ci-mongo" ]
-  
-  ci-mongo:
-    image: mongo:2
-    command:
-      - "--smallfiles"
+  mongo:
+    image: mongo:3.6.23
     ports:
       - "27017:27017"
 
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
new file mode 100644
index 0000000..4ac3234
--- /dev/null
+++ b/gradle/libs.versions.toml
@@ -0,0 +1,2 @@
+# This file was generated by the Gradle 'init' task.
+# https://docs.gradle.org/current/userguide/platforms.html#sub::toml-dependencies-format
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 0000000..e644113
Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 0000000..b82aa23
--- /dev/null
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,7 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
new file mode 100755
index 0000000..1aa94a4
--- /dev/null
+++ b/gradlew
@@ -0,0 +1,249 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# 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
+#
+#      https://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.
+#
+
+##############################################################################
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
+done
+
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&2
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD=$JAVA_HOME/jre/sh/java
+    else
+        JAVACMD=$JAVA_HOME/bin/java
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
+exec "$JAVACMD" "$@"
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 0000000..19e74eb
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1,8 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * The settings file is used to specify which projects to include in your build.
+ * For more detailed information on multi-project builds, please refer to https://docs.gradle.org/8.7/userguide/multi_project_builds.html in the Gradle documentation.
+ */
+
+rootProject.name = 'AssemblyHomologyService'
diff --git a/src/us/kbase/assemblyhomology/config/AssemblyHomologyConfig.java b/src/us/kbase/assemblyhomology/config/AssemblyHomologyConfig.java
index 7c8d5cc..0a5dc8e 100644
--- a/src/us/kbase/assemblyhomology/config/AssemblyHomologyConfig.java
+++ b/src/us/kbase/assemblyhomology/config/AssemblyHomologyConfig.java
@@ -32,8 +32,8 @@
  * mongo-pwd
  * temp-dir
  * filters
- * filter-<name>-factory-class
- * filter-<name>-init-<key>
+ * filter-&lt;name&gt;-factory-class
+ * filter-&lt;name&gt;-init-&lt;key&gt;
  * dont-trust-x-ip-headers
  * </pre>
  * 
@@ -123,6 +123,7 @@ private AssemblyHomologyConfig(
 		if (nullLogger) {
 			logger = new NullLogger();
 		} else {
+			JsonServerSyslog.setStaticUseSyslog(false);
 			// may want to allow configuring the logger name, but YAGNI
 			logger = new JsonServerSysLogAutoLogger(new JsonServerSyslog(LOG_NAME,
 					//TODO KBASECOMMON allow null for the fake config prop arg
diff --git a/src/us/kbase/assemblyhomology/core/AssemblyHomology.java b/src/us/kbase/assemblyhomology/core/AssemblyHomology.java
index ca3652e..cd21e3b 100644
--- a/src/us/kbase/assemblyhomology/core/AssemblyHomology.java
+++ b/src/us/kbase/assemblyhomology/core/AssemblyHomology.java
@@ -178,8 +178,8 @@ public Optional<Path> getExpectedFileExtension(final MinHashImplementationName i
 	 * @param namespaceIDs the namespace IDs for the namespaces of interest.
 	 * @param sketchDB the input query sketch that will be measured against the sketch databases
 	 * associated with the given sequences.
-	 * @param returnCount the number of measurements to return. If < 1 or > 1000, 10 measurements
-	 * will be returned.
+	 * @param returnCount the number of measurements to return. If &lt; 1 or &gt; 1000,
+	 * 10 measurements will be returned.
 	 * @param strict true to enforce an exact match between sketch parameters. If false, 
 	 * differences in the parameters will be ignored if the MinHash implementation allows it.
 	 * @param token a token to use for namespaces that accept or require authentication. Pass null
diff --git a/src/us/kbase/assemblyhomology/load/NamespaceLoadInfo.java b/src/us/kbase/assemblyhomology/load/NamespaceLoadInfo.java
index fae3589..b0c4906 100644
--- a/src/us/kbase/assemblyhomology/load/NamespaceLoadInfo.java
+++ b/src/us/kbase/assemblyhomology/load/NamespaceLoadInfo.java
@@ -30,7 +30,7 @@
  * sourcedatabase: CI Refdata
  * description: some reference data
  * filterid: myfilter
- * <pre>
+ * </pre>
  * 
  * @author gaprice@lbl.gov
  *
diff --git a/src/us/kbase/assemblyhomology/service/api/Namespaces.java b/src/us/kbase/assemblyhomology/service/api/Namespaces.java
index ff9c953..c6fdba2 100644
--- a/src/us/kbase/assemblyhomology/service/api/Namespaces.java
+++ b/src/us/kbase/assemblyhomology/service/api/Namespaces.java
@@ -117,11 +117,12 @@ private Map<String, Object> fromNamespace(final NamespaceView ns) {
 	
 	/** Search one or more namespaces. Expects a sketch database file in the request body.
 	 * @param request the incoming servlet request.
+	 * @param auth the authorization token.
 	 * @param namespaces a comma delimited string of namespace IDs.
 	 * @param notStrict if non null, MinHash searches will continue if possible if the query
 	 * sketch database parameters do not match the target database parameters.
-	 * @param max the maximum number of matches to return. If missing, < 1, or > 100 the maximum
-	 * is set to 10.
+	 * @param max the maximum number of matches to return. If missing, &lt; 1, or &gt;
+	 * 100 the maximum is set to 10.
 	 * @return the matches.
 	 * @throws IOException if an error occurs retrieving the sketch database file from the
 	 * request or saving the file to a temporary file.
diff --git a/src/us/kbase/assemblyhomology/storage/AssemblyHomologyStorage.java b/src/us/kbase/assemblyhomology/storage/AssemblyHomologyStorage.java
index f1f6b9e..92f643e 100644
--- a/src/us/kbase/assemblyhomology/storage/AssemblyHomologyStorage.java
+++ b/src/us/kbase/assemblyhomology/storage/AssemblyHomologyStorage.java
@@ -67,6 +67,7 @@ List<SequenceMetadata> getSequenceMetadata(NamespaceID namespaceID, List<String>
 	 * storage system fails.
 	 * @throws NoSuchSequenceException if the requested sequence id(s) does not exist within the
 	 * namespace and its current load ID.
+	 * @throws NoSuchNamespaceException if the provided namespace does not exist.
 	 */
 	List<SequenceMetadata> getSequenceMetadata(
 			NamespaceID namespaceID,
diff --git a/src/us/kbase/assemblyhomology/util/Restreamable.java b/src/us/kbase/assemblyhomology/util/Restreamable.java
index 8b90a18..5f08347 100644
--- a/src/us/kbase/assemblyhomology/util/Restreamable.java
+++ b/src/us/kbase/assemblyhomology/util/Restreamable.java
@@ -17,7 +17,9 @@ public interface Restreamable {
 	 */
 	InputStream getInputStream() throws IOException;
 	
-	/** Get information about the source of a stream. Typically a file name. */
+	/** Get information about the source of a stream. Typically a file name.
+	 * @return the source information. 
+	 */
 	String getSourceInfo();
 	
 }
diff --git a/src/us/kbase/assemblyhomology/util/Util.java b/src/us/kbase/assemblyhomology/util/Util.java
index c036c52..03ca5e1 100644
--- a/src/us/kbase/assemblyhomology/util/Util.java
+++ b/src/us/kbase/assemblyhomology/util/Util.java
@@ -86,6 +86,7 @@ private static int codePoints(final String s) {
 	}
 	
 	/** Check that the provided collection is not null and contains no null elements.
+	 * @param <T> the type of the collecction items.
 	 * @param col the collection to test.
 	 * @param name the name of the collection to use in any error messages.
 	 */
@@ -115,7 +116,7 @@ public static void checkNoNullsOrEmpties(final Collection<String> strings, final
 	
 	
 	/** Load and instantiate a class with a given interface. Expects a constructor that takes
-	 * a single Map<String, String> argument.
+	 * a single Map&lt;String, String&gt; argument.
 	 * @param <T> the class that will be instantiated.
 	 * @param className the fully qualified class name.
 	 * @param interfce the required interface.
diff --git a/src/us/kbase/test/assemblyhomology/MongoStorageTestManager.java b/src/us/kbase/test/assemblyhomology/MongoStorageTestManager.java
index 11fddc7..d60c2cb 100644
--- a/src/us/kbase/test/assemblyhomology/MongoStorageTestManager.java
+++ b/src/us/kbase/test/assemblyhomology/MongoStorageTestManager.java
@@ -13,7 +13,7 @@
 import com.mongodb.client.MongoDatabase;
 
 import us.kbase.assemblyhomology.storage.mongo.MongoAssemblyHomologyStorage;
-import us.kbase.common.test.controllers.mongo.MongoController;
+import us.kbase.testutils.controllers.mongo.MongoController;
 
 public class MongoStorageTestManager {
 
diff --git a/src/us/kbase/test/assemblyhomology/TestCommon.java b/src/us/kbase/test/assemblyhomology/TestCommon.java
index 7b2a343..5462889 100644
--- a/src/us/kbase/test/assemblyhomology/TestCommon.java
+++ b/src/us/kbase/test/assemblyhomology/TestCommon.java
@@ -40,7 +40,7 @@
 import ch.qos.logback.classic.spi.ILoggingEvent;
 import ch.qos.logback.classic.spi.IThrowableProxy;
 import ch.qos.logback.core.AppenderBase;
-import us.kbase.common.test.TestException;
+import us.kbase.testutils.TestException;
 
 public class TestCommon {
 
diff --git a/src/us/kbase/test/assemblyhomology/controllers/workspace/WorkspaceController.java b/src/us/kbase/test/assemblyhomology/controllers/workspace/WorkspaceController.java
index 188db06..b4d2eb0 100644
--- a/src/us/kbase/test/assemblyhomology/controllers/workspace/WorkspaceController.java
+++ b/src/us/kbase/test/assemblyhomology/controllers/workspace/WorkspaceController.java
@@ -1,7 +1,7 @@
 package us.kbase.test.assemblyhomology.controllers.workspace;
 
-import static us.kbase.common.test.controllers.ControllerCommon.findFreePort;
-import static us.kbase.common.test.controllers.ControllerCommon.makeTempDirs;
+import static us.kbase.testutils.controllers.ControllerCommon.findFreePort;
+import static us.kbase.testutils.controllers.ControllerCommon.makeTempDirs;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -27,7 +27,7 @@
 import com.mongodb.MongoClient;
 import com.mongodb.client.MongoDatabase;
 
-import us.kbase.common.test.TestException;
+import us.kbase.testutils.TestException;
 
 
 /** Q&D Utility to run a Workspace server for the purposes of testing from
diff --git a/src/us/kbase/test/assemblyhomology/core/AssemblyHomologyTest.java b/src/us/kbase/test/assemblyhomology/core/AssemblyHomologyTest.java
index dce5ca3..acf2961 100644
--- a/src/us/kbase/test/assemblyhomology/core/AssemblyHomologyTest.java
+++ b/src/us/kbase/test/assemblyhomology/core/AssemblyHomologyTest.java
@@ -77,7 +77,7 @@
 import us.kbase.assemblyhomology.minhash.exceptions.MinHashInitException;
 import us.kbase.assemblyhomology.minhash.exceptions.NotASketchException;
 import us.kbase.assemblyhomology.storage.AssemblyHomologyStorage;
-import us.kbase.common.test.TestException;
+import us.kbase.testutils.TestException;
 import us.kbase.test.assemblyhomology.TestCommon;
 import us.kbase.test.assemblyhomology.TestCommon.LogEvent;
 
diff --git a/src/us/kbase/test/assemblyhomology/data/TestDataManager.java b/src/us/kbase/test/assemblyhomology/data/TestDataManager.java
index 5684577..b0f2403 100644
--- a/src/us/kbase/test/assemblyhomology/data/TestDataManager.java
+++ b/src/us/kbase/test/assemblyhomology/data/TestDataManager.java
@@ -7,7 +7,7 @@
 
 import org.apache.commons.io.IOUtils;
 
-import us.kbase.common.test.TestException;
+import us.kbase.testutils.TestException;
 
 public class TestDataManager {
 
diff --git a/src/us/kbase/test/assemblyhomology/integration/ServiceIntegrationTest.java b/src/us/kbase/test/assemblyhomology/integration/ServiceIntegrationTest.java
index e3d9d7e..8226ccf 100644
--- a/src/us/kbase/test/assemblyhomology/integration/ServiceIntegrationTest.java
+++ b/src/us/kbase/test/assemblyhomology/integration/ServiceIntegrationTest.java
@@ -66,7 +66,7 @@
 import us.kbase.assemblyhomology.minhash.MinHashSketchDatabase;
 import us.kbase.assemblyhomology.minhash.exceptions.MinHashDistanceFilterAuthenticationException;
 import us.kbase.auth.AuthToken;
-import us.kbase.common.test.RegexMatcher;
+import us.kbase.testutils.RegexMatcher;
 import us.kbase.test.assemblyhomology.MapBuilder;
 import us.kbase.test.assemblyhomology.MongoStorageTestManager;
 import us.kbase.test.assemblyhomology.StandaloneAssemblyHomologyServer;