Merge pull request #91 from kbase/dev-gradle

Add gradle

.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
+

.github/workflows/test.yml

@@ -26,7 +26,7 @@ jobs:
           - java: '8'
             mongo: 'mongodb-linux-x86_64-3.6.13'
             wired_tiger: 'false'
-            ant_test: 'test'
+            gradle_test: 'test'
     steps:
       - uses: actions/checkout@v3
 
@@ -44,10 +44,6 @@ jobs:
           # move to parent dir of homedir to install binaries etc
           cd ..
 
-          # set up jars
-          git clone https://github.com/kbase/jars
-          export JARSDIR=$(pwd)/jars/lib/jars/
-
           # set up mongo
           wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz
           tar xfz ${{matrix.mongo}}.tgz
@@ -62,11 +58,10 @@ jobs:
       - name: Run tests
         shell: bash
         run: |
-          ant ${{matrix.ant_test}}
+          ./gradlew ${{matrix.gradle_test}}
 
-# TODO reinstate coverage upload w/ Gradle, ant is not configured for it
-#      - name: Upload coverage to Codecov
-#        uses: codecov/codecov-action@v3
-#        with:
-#          token: ${{ secrets.CODECOV_TOKEN }}
-#          fail_ci_if_error: true
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

README.md

@@ -1,19 +1,13 @@
-**master:** [![Build Status](https://travis-ci.org/kbase/narrative_method_store.svg?branch=master)](https://travis-ci.org/kbase/narrative_method_store) | **staging:** [![Build Status](https://travis-ci.org/kbase/narrative_method_store.svg?branch=staging)](https://travis-ci.org/kbase/narrative_method_store) | **develop:** [![Build Status](https://travis-ci.org/kbase/narrative_method_store.svg?branch=develop)](https://travis-ci.org/kbase/narrative_method_store)
-
 Narrative Method Store
 ======================
 
 A KBase service for dynamically listing and accessing specifications and documentation for Narrative methods, apps, types, and categories of methods/apps.  The Narrative Interface loads available methods/apps from this service.  Specifications and documentation are pulled from a github repo named [narrative_method_specs](https://github.com/kbase/narrative_method_specs).  Updates to specifications and documentation on the configured branch are reflected by this service within some referesh rate, usually set to every 1-2 minutes.  Additional documentation on how to construct a specification can be found in the narrative_method_specs repository.
 
-The Narrative Method Store has a CLI for developers and documenters to check the status of the method store, list and fetch specifications and documentation, and validate local changes to specifications/documentation.  Instructions on deploying the CLI can be found at [docs/CLI_Deployment_Guide.md](docs/CLI_Deployment_Guide.md).
-
-The Narrative Method Store can be deployed within a standard KBase runtime environment with the standard KBase deployment process. Briefly, from within the dev_container, clone this repo into the modules directory.  Rebuild any environment variables by running the dev_container bootstrap script and sourcing the user-env.sh file.  Within this repo directory, run `make`, optionally `make test`, and finally `make deploy TARGET=[deployment_directory]`.
-
 Test requirements:
 
 * The `mongod` executable must be on the path
 
 To run tests:
 
 * Copy `test.cfg.example` to `test.cfg` and make any adjustments necessary
-* `ant test`
+* `./gradlew test`

RELEASE_NOTES.txt

@@ -8,6 +8,7 @@ VERSION: 0.3.12 (Released TBD)
 
 UPDATED FEATURES:
 - Added the `exact_match_on` field to the dynamic dropdown options.
+- Changed the build system from Make / Ant to Gradle.
 
 VERSION: 0.3.11 (Released 6/29/2021)
 ------------------------------------

build.gradle

@@ -0,0 +1,260 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+	id 'java'
+	id 'war'
+	id 'jacoco'
+}
+
+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 update dockerfile
+// TODO NOW delete build.xml and Makefile
+// TODO NOW run tests from Eclipse w/o specifying classpath manually & remove sourceSets & classpath
+
+repositories {
+	mavenCentral()
+}
+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
+}
+
+javadoc {
+	/* We don't actually need the full javadoc for anything, so just hijack this task for
+	 * building the client javadocs. If we ever need the full javadocs make a new task for the
+	 * client java docs
+	 */
+	// TODO DOCS currently java-common and auth links don't work. ROI for fixing them is low.
+	failOnError = false  // fixing this would be a lot of work
+	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/"
+	}
+	include "**/narrativemethodstore/*.java"
+	exclude "**/narrativemethodstore/NarrativeMethodStoreServer.java"
+	exclude "**/narrativemethodstore/ImageServlet.java"
+	include "**/common/service/Tuple*.java"
+}
+
+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
+	systemProperty "test.cfg", "./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
+	}
+}
+
+jar {
+	// Much like javadoc, we hijack this task to build the client jar, since we don't need
+	// a service jar
+	include "us/kbase/narrativemethodstore/*.class"
+	exclude "us/kbase/narrativemethodstore/NarrativeMethodStoreServer*.class"  // exclude anonymous classes
+	exclude "us/kbase/narrativemethodstore/ImageServlet*.class"  // exclude anonymous classes
+	include "us/kbase/common/service/Tuple*.class"
+	archiveAppendix = 'client'
+}
+
+war {
+	webXml = file('war/web.xml')
+}
+
+/* SDK compile notes:
+ * kb-sdk starts a docker container in interactive mode. Gradle's commandLine doesn't allocate
+ * a tty so the command fails.
+ * I tried using a ProcessBuilder and
+ * https://docs.oracle.com/en%2Fjava%2Fjavase%2F11%2Fdocs%2Fapi%2F%2F/java.base/java/lang/ProcessBuilder.html#inheritIO()
+ * but that failed also with no useful output.
+ * 
+ * The current solution is to precede the kb-sdk call with a script call, which either
+ * allocates a tty or fools kb-sdk into thinking there is one - not quite sure.
+ * https://man7.org/linux/man-pages/man1/script.1.html
+ * I tried to redirect the script log file  to /dev/null with -O and --log-out but script didn't
+ * recognize either option, hence the delete.
+ *
+ * This is, generally speaking, a janky mess and if someone can find a better way to do this
+ * that'd be fantastic.
+ */
+
+ var LOC_SCRIPT_TYPESCRIPT = "$rootDir/typescript"
+
+// TODO GRADLE is there some way to DRY these 3 compile tasks up? Not a huge deal
+task sdkCompileHTML {
+	// We want to check in the HTML so we don't put it in the build dir
+	var cmd = "kb-sdk compile --html --out $LOC_DOC_HTML $LOC_NMS_SPEC"
+	doLast {
+		exec {
+			commandLine "script", "-qefc", cmd
+		}
+		delete LOC_SCRIPT_TYPESCRIPT
+	}
+}
+
+task sdkCompileLibs {
+	var cmd = "kb-sdk compile " +
+				"--out lib " +
+				"--jsclname javascript/NarrativeMethodStore/Client " +
+				"--plclname Bio::KBase::NarrativeMethodStore::Client " +
+				"--pyclname biokbase.narrative_method_store.client " +
+				"--url $DEFAULT_URL " + 
+				LOC_NMS_SPEC
+	doLast {
+		exec {
+			commandLine "script", "-qefc", cmd
+		}
+		delete LOC_SCRIPT_TYPESCRIPT
+		delete "$rootDir/lib/biokbase/narrative_method_store/authclient.py"
+	}
+}
+
+task sdkCompileJava {
+	// TODO GRADLE is there a variable for src/main/java when we move the code locations?
+	var cmd = "kb-sdk compile " +
+				"--java " +
+				"--javasrc $rootDir/src " +
+				"--javasrv " +
+				"--out . " +
+				"--url $DEFAULT_URL " + 
+				LOC_NMS_SPEC
+	doLast {
+		exec {
+			commandLine "script", "-qefc", cmd
+		}
+		delete LOC_SCRIPT_TYPESCRIPT
+	}
+}
+
+task sdkCompile {
+	dependsOn sdkCompileHTML
+	dependsOn sdkCompileJava
+	dependsOn sdkCompileLibs
+}
+
+// Custom java project layout
+sourceSets {
+	main {
+		java {
+			srcDirs = ["src"]
+			exclude '**/test/**'
+		}
+	}
+	test {
+		java {
+			srcDirs = ["src"]
+			include '**/test/**'
+		}
+		resources {
+			srcDirs = ["src"]
+			include "**/*.properties"
+		}
+	}
+}
+
+configurations {
+	// can't directly access testImplementation, so extend and access
+	testimpl.extendsFrom testImplementation
+}
+
+def fromURL = { url, name ->
+	File file = new File("$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 fromURL(
+		'https://github.com/kbase/jars/raw/master/lib/jars/kbase/auth/kbase-auth-0.4.4.jar',
+		'kbase-auth-0.4.4'
+	)
+	implementation 'org.ini4j:ini4j:0.5.2'
+	implementation 'com.fasterxml.jackson.core:jackson-annotations:2.2.3'
+	implementation 'com.fasterxml.jackson.core:jackson-databind:2.2.3'
+	implementation 'org.mongodb:mongo-java-driver:3.10.1'
+	implementation 'com.github.docker-java:docker-java:1.3.0'
+	implementation 'org.yaml:snakeyaml:1.11'
+	implementation 'org.apache.velocity:velocity:1.7'
+
+	// ###
+	// Server dependencies, specifically for java_common JsonServerServlet and
+	// NarrativeMethodServer
+	// ###
+
+	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:1.7.7'
+	// 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.
+	implementation fromURL(
+		'https://github.com/kbase/jars/raw/master/lib/jars/syslog4j/syslog4j-0.9.46.jar',
+		'syslog4j-0.9.46'
+	)
+	implementation 'javax.annotation:javax.annotation-api:1.2'
+	implementation 'javax.servlet:servlet-api:2.5'
+	// joda-time is required for kbase-common and syslog4j
+	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'
+	// needed for syslog4j
+	implementation 'net.java.dev.jna:jna:3.4.0'
+
+	// ### Blobstore / Shock client and dependencies ###
+	// TODO BUILD can the code that uses these be removed? I don't think the NMS
+	//            talks to Shock any more
+
+	implementation fromURL(
+		'https://github.com/kbase/jars/raw/master/lib/jars/kbase/shock/shock-client-0.0.15.jar',
+		'shock-client-0.0.15'
+	)
+	implementation 'org.apache.httpcomponents:httpclient:4.3.1'
+	implementation 'org.apache.httpcomponents:httpmime:4.3.1'
+
+	// ### Test ###
+
+	testImplementation 'junit:junit:4.12'
+	testImplementation 'org.mockito:mockito-core:3.0.0'
+	testImplementation 'org.apache.commons:commons-lang3:3.5'
+}
+
+task showTestClassPath {
+	doLast {
+		configurations.testimpl.each { println it }
+	}
+}
+