DO NOT MERGE

.codecov.yml

@@ -26,5 +26,4 @@ comment:
   require_changes: no
 
 ignore:
-  - "build"
   - "deployment"

.gitattributes

@@ -0,0 +1,6 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# These are explicitly windows files and should use crlf
+*.bat           text eol=crlf
+

.github/workflows/test.yml

@@ -19,10 +19,8 @@ jobs:
   auth2_tests:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        # Note that there's a mongo-only ant test directive. Use that for all mongo versions
-        # except for one if there's > 1 mongo version to test. No need for testing code that
-        # doesn't touch mongo against multiple mongo versions
         include:
           - java: '8'
             mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
@@ -40,13 +38,6 @@ jobs:
           distribution: 'temurin'
           java-version: ${{matrix.java}}
 
-      - name: Clone jars as sister repo
-        shell: bash
-        run: |
-          cd ..
-          git clone https://github.com/kbase/jars
-          cd -
-
       - name: Install mongo and set up test config
         shell: bash
         run: |
@@ -62,7 +53,7 @@ jobs:
           cat test.cfg
 
       - name: Run tests
-        run: ant test
+        run: ./gradlew test
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

Dockerfile

@@ -1,10 +1,7 @@
 FROM kbase/sdkbase2 as build
 
 COPY . /tmp/auth2
-RUN cd /tmp \
-    && git clone https://github.com/kbase/jars \
-    && cd auth2 \
-    && ant buildwar
+RUN cd /tmp/auth2 && ./gradlew war
 
 FROM kbase/kb_jre:latest
 
@@ -15,6 +12,8 @@ ARG BRANCH=develop
 
 COPY --from=build /tmp/auth2/deployment/ /kb/deployment/
 COPY --from=build /tmp/auth2/jettybase/ /kb/deployment/jettybase/
+COPY --from=build /tmp/auth2/build/libs/auth2.war /kb/deployment/jettybase/webapps/ROOT.war
+COPY --from=build /tmp/auth2/templates /kb/deployment/jettybase/templates
 
 # The BUILD_DATE value seem to bust the docker cache when the timestamp changes, move to
 # the end

README.md

@@ -235,24 +235,33 @@ Removes all test mode data from the system.
 ## 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/kbase/auth2)  
-The jars repo (git clone https://github.com/kbase/jars)  
-The two repos above need to be in the same parent folder.
 
 ## To start server
 
 start mongodb  
 if using mongo auth, create a mongo user  
-cd into the auth2 repo  
-`ant build`  
-copy `deploy.cfg.example` to `deploy.cfg` and fill in appropriately  
-`export KB_DEPLOYMENT_CONFIG=<path to deploy.cfg>`  
-`cd jettybase`  
-`./jettybase$ java -jar -Djetty.port=<port> <path to jetty install>/start.jar`  
+cd into the auth2 repo
+
+```
+./gradlew war
+mkdir -p jettybase/webapps
+cp build/libs/auth2.war jettybase/webapps/ROOT.war
+cp templates jettybase/templates
+```
+
+copy `deploy.cfg.example` to `deploy.cfg` and fill in appropriately
+
+```
+export KB_DEPLOYMENT_CONFIG=<path to deploy.cfg>
+cd jettybase
+./jettybase$ java -jar -Djetty.port=<port> <path to jetty install>/start.jar
+```
+
+Or just use the Docker build, which is probably a lot easier.
 
 ## Administer the server
 

build.gradle

@@ -0,0 +1,176 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * This generated file contains a sample Java application project to get you started.
+ * For more details take a look at the 'Building Java & JVM projects' chapter in the Gradle
+ * User Manual available at https://docs.gradle.org/7.4.2/userguide/building_java_projects.html
+ */
+
+plugins {
+	id 'java'
+	id 'war'
+	id 'jacoco'
+	id 'org.ajoberstar.grgit' version '4.1.1'
+}
+
+repositories {
+	mavenCentral()
+}
+
+task getGitCommitId {
+    doLast {
+        def commitId = grgit.head().id
+        file('src/us/kbase/auth2/gitcommit').text = commitId
+    }
+}
+
+compileJava {
+	dependsOn getGitCommitId
+	if (JavaVersion.current() <= JavaVersion.VERSION_1_8) {
+		// TODO BUILD remove when we no longer support java 8
+		java.sourceCompatibility = JavaVersion.VERSION_1_8
+		java.targetCompatibility = JavaVersion.VERSION_1_8
+	} else {
+		options.release = 8
+	}
+}
+
+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
+	  * mong tests with matrixed mongo versions. Combine coverage at the end somehow
+	*/
+	systemProperty "AUTH2_TEST_CONFIG", "./test.cfg"
+	testLogging {
+		exceptionFormat = 'full'
+		showStandardStreams = true
+	}
+	finalizedBy jacocoTestReport
+}
+
+jacocoTestReport {
+	reports {
+		xml.required = true
+		csv.required = true
+	}
+}
+
+// TODO NOW javadocs
+// TODO NOW run tests from Eclipse w/o specifying classpath manually
+// TODO NOW make auth, test, and template jars
+// TODO NOW make script
+// TODO NOW test server starts in docker container, including templates when gradle done
+
+// Custom java project layout
+sourceSets {
+	main {
+		java {
+			srcDirs = ["src"]
+			exclude '**/test/**'
+		}
+		resources {
+			srcDirs = ["src"]
+			include "**/gitcommit"
+		}
+	}
+	test {
+		java {
+			srcDirs = ["src"]
+			include '**/test/**'
+		}
+		resources {
+			srcDirs = ["src"]
+			include "**/*.testdata"
+			include "**/authjars"
+		}
+	}
+}
+
+war {
+	webXml = file('war/web.xml')
+	// For some reason the test directories are included in the war file
+	// although the files are gone. Not sure why
+}
+
+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 {
+
+	// ### General application dependencies ###
+
+	implementation 'commons-codec:commons-codec:1.8'
+	implementation 'commons-validator:commons-validator:1.5.1'
+	implementation 'com.google.guava:guava:18.0'
+	implementation 'org.ini4j:ini4j:0.5.2'
+	implementation 'com.beust:jcommander:1.48'
+	implementation 'org.mongodb:mongodb-driver-core:4.11.1'
+	implementation 'org.mongodb:mongodb-driver-sync:4.11.1'
+	implementation 'org.mongodb:bson-record-codec:4.11.1'
+	implementation 'org.mongodb:bson:4.11.1'
+	implementation 'com.github.spullara.mustache.java:compiler:0.9.3'
+	implementation 'com.nulab-inc:zxcvbn:1.2.2'
+	implementation 'nl.basjes.parse.useragent:yauaa:1.3'
+	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 'com.github.zafarkhaja:java-semver:0.9.0'
+	implementation 'org.glassfish.jersey.containers:jersey-container-servlet:2.23.2'
+	implementation 'org.glassfish.jersey.media:jersey-media-json-jackson:2.23.2'
+	implementation 'org.glassfish.jersey.ext:jersey-mvc-mustache:2.23.2'
+	implementation 'javax.persistence:persistence-api:1.0'
+	implementation 'javax.servlet:javax.servlet-api:3.0.1'
+	implementation 'javax.xml.bind:jaxb-api:2.4.0-b180830.0359'
+
+
+	// ### Logging dependencies ###
+	implementation fromURL(
+		'https://github.com/kbase/jars/raw/master/lib/jars/kbase/common/kbase-common-0.0.22.jar',
+		'kbase-common-0.0.22'
+	)
+	implementation 'ch.qos.logback:logback-classic:1.1.2'
+	implementation 'org.slf4j:slf4j-api:1.7.25'
+	// Syslog4j 0.9.46 doesn't appear to be available on Maven. It apparently lives in 
+	// a JetBrains artifact server, but that's too much trouble and there's only one version there
+	// anyway.
+	// https://mvnrepository.com/artifact/org.jetbrains/syslog4j/0.9.46
+	// 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 fromURL(
+		'https://github.com/kbase/jars/raw/master/lib/jars/syslog4j/syslog4j-0.9.46.jar',
+		'syslog4j-0.9.46'
+	)
+	// needed for syslog
+	implementation 'net.java.dev.jna:jna:3.4.0'
+
+	// ### Test ###
+
+	testImplementation 'commons-io:commons-io:2.4'
+	testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10'
+	testImplementation 'junit:junit:4.12'
+	testImplementation 'org.mock-server:mockserver-netty:3.10.4'
+	testImplementation 'org.eclipse.jetty:jetty-server:9.3.11.v20160721'
+	testImplementation 'org.eclipse.jetty:jetty-servlet:9.3.11.v20160721'
+	testImplementation 'io.github.java-diff-utils:java-diff-utils:2.2.0'
+	testImplementation 'de.danielbechler:java-object-diff:0.94'
+	testImplementation 'org.jsoup:jsoup:1.10.2'
+	testImplementation 'org.mockito:mockito-core:3.0.0'
+}

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists