kbase · MrCreosote · Sep 10, 2025 · Jun 12, 2025 · Jun 16, 2025 · Sep 4, 2025
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,12 @@
+#
+# 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
+
+# Binary files should be left untouched
+*.jar           binary
+
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,14 +1,26 @@
 version: 2
 updates:
-- package-ecosystem: docker
-  directory: "/"
-  schedule:
-    interval: weekly
-    time: '11:00'
-  open-pull-requests-limit: 10
-- package-ecosystem: pip
-  directory: "/"
-  schedule:
-    interval: weekly
-    time: '11:00'
-  open-pull-requests-limit: 10
+
+  # Docker base image updates
+  - package-ecosystem: docker
+    directory: "/"
+    schedule:
+      interval: monthly
+      time: "11:00"
+    open-pull-requests-limit: 25
+
+  # Python (pip) dependencies
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: monthly
+      time: "11:00"
+    open-pull-requests-limit: 25
+
+  # GitHub Actions dependencies
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows"
+    schedule:
+      interval: monthly
+      time: "11:00"
+    open-pull-requests-limit: 25
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,7 @@
+/bin/
+
+# Ignore Gradle project-specific cache directory
+.gradle
+
+# Ignore Gradle build output directory
+build
diff --git a/Catalog.html b/Catalog.html
diff --git a/KIDLspec.css b/KIDLspec.css
@@ -0,0 +1,65 @@
+html, body {
+	height: 100%;
+}
+html {
+	display: table;
+	margin: auto;
+}
+body {
+	background-color: white;
+	color: #000;
+	font-family: Menlo, Monaco, Consolas, "Courier New", monospace;
+	font-weight: normal;
+	font-size: 12px;
+	margin: 0;
+	padding: 20px;
+	display: table-cell;
+	vertical-align: middle;
+}
+span.space {
+	display: inline-block;
+	width: 7px;
+}
+span.tab {
+	display: inline-block;
+	width: 30px;
+}
+span.keyword {
+	font-weight: bold;
+	color: #008;
+}
+span.name {
+	color: #000; !important
+}
+span.deprecated {
+	text-decoration: line-through;
+}
+span.annotation {
+	color: #303030;
+}
+span.primitive {
+	font-weight: bold;
+	color: #066;
+}
+div.body {
+	background-color: #ffffff;
+	color: #3e4349;
+	padding: 0 30px;
+}
+div.comment {
+	color: #A0A0A0;
+}
+a {
+	color: #004b6b;
+	text-decoration: none;
+}
+a:hover {
+	color: #6d4100;
+	text-decoration: underline;
+}
+:target {
+	background-color: #ffa;
+}
+div.body p, div.body dd, div.body li {
+	line-height: 1.4em;
+}
diff --git a/Makefile b/Makefile
@@ -5,7 +5,6 @@ SERVICE_CAPS = Catalog
 #$(shell perl server_scripts/get_deploy_cfg.pm $(SERVICE_CAPS).port)
 SERVICE_PORT = 5000
 SPEC_FILE = catalog.spec
-URL = https://kbase.us/services/catalog/rpc
 
 #End of user defined variables
 
@@ -29,18 +28,18 @@ PATH := kb_sdk/bin:$(PATH)
 
 
 compile-kb-module:
+	kb-sdk compile $(SPEC_FILE) \
+		--out . \
+		--html
 	kb-sdk compile $(SPEC_FILE) \
 		--out $(LIB_DIR) \
-		--plclname Bio::KBase::$(SERVICE_CAPS)::Client \
-		--jsclname javascript/Client \
 		--pyclname biokbase.$(SERVICE).Client \
-		--javasrc java \
-		--java \
 		--pysrvname biokbase.$(SERVICE).Server \
-		--pyimplname biokbase.$(SERVICE).Impl;
-	touch $(LIB_DIR)/biokbase/__init__.py
-	touch $(LIB_DIR)/biokbase/$(SERVICE)/__init__.py
-
+		--pyimplname biokbase.$(SERVICE).Impl
+	kb-sdk compile $(SPEC_FILE) \
+		--out . \
+		--java \
+		--javasrc src/main/java
 
 # start/stop the service running out of THIS directory
 build-local-server-control-scripts:

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,5 +1,8 @@
 # Catalog Service release notes
 
+## v2.3.1 - 9/3/2025
+  - Added a JITPack build for the catalog client
+
 ## v2.3.0 - 3/5/2025
   - Removed all submodules(jars, kbapi_common, nms) as part of repository clean up.
   - The MongoDB clients have been updated to the most recent version and the service tested against Mongo 7.

diff --git a/build.gradle b/build.gradle
@@ -0,0 +1,60 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+	id 'java'
+	id 'maven-publish'
+}
+
+group = 'com.github.kbase'
+
+var VER_AUTH2_CLIENT = "0.5.0"
+var VER_JAVA_COMMON = "0.3.0"
+
+repositories {
+	mavenCentral()
+	maven {
+		name = "JitPack" 
+		url = 'https://jitpack.io'
+	}
+}
+
+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
+}
+
+java {
+	withSourcesJar()
+	withJavadocJar()
+}
+
+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/11/docs/api/"
+		links "https://javadoc.jitpack.io/com/github/kbase/auth2_client_java/$VER_AUTH2_CLIENT/javadoc/"
+		links "https://javadoc.jitpack.io/com/github/kbase/java_common/$VER_JAVA_COMMON/javadoc/"
+	}
+}
+
+publishing {
+	publications {
+		maven(MavenPublication) {
+			from components.java
+		}
+	}
+}
+
+dependencies {
+
+	// using older dependencies to not force upgrades on services that might not be able to
+	// handle them. Need to upgrade the services and then upgrade here
+	implementation "com.github.kbase:java_common:$VER_JAVA_COMMON"
+	implementation "com.fasterxml.jackson.core:jackson-databind:2.5.4"
+	implementation "com.github.kbase:auth2_client_java:$VER_AUTH2_CLIENT"
+	implementation 'javax.annotation:javax.annotation-api:1.3.2'
+
+}
diff --git a/gradle.properties b/gradle.properties
@@ -0,0 +1,5 @@
+# This file was generated by the Gradle 'init' task.
+# https://docs.gradle.org/current/userguide/build_environment.html#sec:gradle_configuration_properties
+
+org.gradle.configuration-cache=true
+
diff --git a/gradle/libs.versions.toml 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
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,7 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.3-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
Original file line number	Diff line number	Diff line change
		@@ -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