Merge pull request #724 from MrCreosote/dev-gradle2

Build docs

build.gradle

@@ -15,7 +15,9 @@ plugins {
 	id 'com.github.johnrengelman.shadow' version '8.1.1'
 }
 
-// TODO NOW test shadow jar works in groups - remove JNA - commit 2
+var buildDocsDir = "$buildDir/docs/otherdoc/"
+
+// TODO NOW test shadow jar works in groups - need test controller - commit 2
 // TODO NOW get docserver working in WAR and test in docker-compose <- edit to start test server - commit 3
 // TODO NOW client jar - commit 4
 // TODO NOW client jar javadoc - needs java_common source - commit 4
@@ -32,6 +34,52 @@ compileJava {
 	options.release = 11
 }
 
+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.
+	 *           Ideally, in the future make github actions publish docs on release and ref them
+	 *           here.
+	 *           https://github.com/marketplace/actions/deploy-publish-javadoc
+	 *           https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-gradle-registry
+	 */
+	/* TODO DOCS the current sdk documenation looks like invalid html to javadoc
+	 *           need to go through and remove
+	 *           also some spots with < / > that need to be wrapped with {@code } in internal code
+	 */
+	failOnError = false
+	options {
+		links "https://docs.oracle.com/en/java/javase/11/docs/api/"
+	}
+	include "**/workspace/*.java"
+	exclude "**/workspace/WorkspaceServer.java"
+	include "**/common/service/Tuple*.java"
+}
+
+task buildDocs {
+	// ideally we'd add the inputs and outputs spec but that's too much work for too little gain
+	dependsOn javadoc
+	doLast {
+		// need to make sure we remove any docs that no longer exist in the source
+		delete "$buildDocsDir"
+		copy {
+			from "$rootDir/workspace.spec" into "$buildDocsDir"
+		}
+		copy {
+			from "$rootDir/docshtml/" into "$buildDocsDir" include "*"
+		}
+		exec {	
+			commandLine "pod2html", "--infile=$rootDir/lib/Bio/KBase/workspace/Client.pm", "--outfile=$buildDocsDir/workspace_perl.html"
+		}
+		exec {
+			commandLine "sphinx-build", "$rootDir/docsource/", "$buildDocsDir"
+		}
+		delete fileTree(".").matching { include "pod2htm*.tmp" }
+	}
+}
+
 tasks.withType(Test) {
 	/* 
 	 * TODO TEST Figure out why tests fail without this and remove. Might have something to do
@@ -114,14 +162,6 @@ sourceSets {
 	}
 }
 
-javadoc {
-	options {
-		links "https://docs.oracle.com/en/java/javase/11/docs/api/"
-		links "https://www.javadoc.io/doc/com.fasterxml.jackson.core/jackson-core/2.9.9/"
-		links "https://www.javadoc.io/doc/com.fasterxml.jackson.core/jackson-databind/2.9.9/"
-	}
-}
-
 war {
 	webXml = file('war/web.xml')
 }
@@ -189,7 +229,7 @@ dependencies {
 		'kbase-common-0.2.0'
 	)
 	// Pull from jars repo vs a maven repository to avoid the JNA dependency
-	// Need to rework the java common logger to not use syslog4j at all since it's abandonware
+	// 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',

lib/Bio/KBase/workspace/Client.pm

@@ -10783,7 +10783,7 @@ compatibility.
 UnspecifiedObject data - The object's data.
 object_metadata metadata - Metadata for object retrieved/
 
-@deprecated Workspaces.ObjectData
+@deprecated Workspace.ObjectData
 
 
 =item Definition

lib/biokbase/workspace/client.py

@@ -914,7 +914,7 @@ def get_object(self, params, context=None):
            the "get_object" function. Provided for backwards compatibility.
            UnspecifiedObject data - The object's data. object_metadata
            metadata - Metadata for object retrieved/ @deprecated
-           Workspaces.ObjectData) -> structure: parameter "data" of
+           Workspace.ObjectData) -> structure: parameter "data" of
            unspecified object, parameter "metadata" of type "object_metadata"
            (Meta data associated with an object stored in a workspace.
            Provided for backwards compatibility. obj_name id - name of the

src/us/kbase/workspace/GetObjectOutput.java

@@ -20,7 +20,7 @@
  * compatibility.
  * UnspecifiedObject data - The object's data.
  * object_metadata metadata - Metadata for object retrieved/
- * @deprecated Workspaces.ObjectData
+ * @deprecated Workspace.ObjectData
  * </pre>
  * 
  */

src/us/kbase/workspace/WorkspaceServer.java

@@ -102,7 +102,7 @@ public class WorkspaceServer extends JsonServerServlet {
     private static final long serialVersionUID = 1L;
     private static final String version = "0.0.1";
     private static final String gitUrl = "https://github.com/mrcreosote/workspace_deluxe";
-    private static final String gitCommitHash = "5154d57474407fb8e21e5bcd238c6db20666fca8";
+    private static final String gitCommitHash = "8d0c78b928ca21c63ad05b0ee7dbe608065d44d1";
 
     //BEGIN_CLASS_HEADER
 	//TODO JAVADOC really low priority, sorry

workspace.spec

@@ -980,7 +980,7 @@ module Workspace {
 		UnspecifiedObject data - The object's data.
 		object_metadata metadata - Metadata for object retrieved/
 
-		@deprecated Workspaces.ObjectData
+		@deprecated Workspace.ObjectData
 	*/
 	typedef structure {
 		UnspecifiedObject data;