Merge pull request #596 from kbase/develop

Release 0.13.1

Author: MrCreosote

docshtml/Workspace.html

@@ -52,7 +52,7 @@
 # The short X.Y version.
 version = '0.13'
 # The full version, including alpha/beta/rc tags.
-release = '0.13.0'
+release = '0.13.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docsource/conf.py

@@ -3,6 +3,14 @@
 Workspace service release notes
 ===============================
 
+VERSION: 0.13.1 (Released 4/27/2022)
+------------------------------------
+
+UPDATES:
+
+* ``save_objects`` will no longer throw an error if an empty ``ProvenanceAction`` is included in
+  the call. Rather, empty ``ProvenanceAction`` instances will be silently omitted from the list.
+
 VERSION: 0.13.0 (Released 4/13/2022)
 ------------------------------------
 

docsource/releasenotes.rst

@@ -9556,8 +9556,11 @@ A provenance action.
         A provenance action (PA) is an action taken while transforming one data
         object to another. There may be several PAs taken in series. A PA is
         typically running a script, running an api command, etc. All of the
-        following fields are optional but at least one field must be present.
-        Furthermore, more information provided equates to better data provenance.
+        following fields are optional, but more information provided equates to
+        better data provenance.
+        
+        If a provenance action has no fields defined at all, it is silently dropped from
+        the list.
         
         resolved_ws_objects should never be set by the user; it is set by the
         workspace service when returning data.

lib/Bio/KBase/workspace/Client.pm

@@ -20,8 +20,11 @@
  *         A provenance action (PA) is an action taken while transforming one data
  *         object to another. There may be several PAs taken in series. A PA is
  *         typically running a script, running an api command, etc. All of the
- *         following fields are optional but at least one field must be present.
- *         Furthermore, more information provided equates to better data provenance.
+ *         following fields are optional, but more information provided equates to
+ *         better data provenance.
+ *         
+ *         If a provenance action has no fields defined at all, it is silently dropped from
+ *         the list.
  *         
  *         resolved_ws_objects should never be set by the user; it is set by the
  *         workspace service when returning data.

lib/biokbase/workspace/client.py

@@ -701,12 +701,11 @@ private List<String> processReferences(
 			}
 		}
 
-		/** Build the {@link ProvenanceAction}. At least one field must be set before the build
-		 * attempt.
-		 * @return the provenance action.
+		/** Check the builder has any fields set.
+		 * @return true if no fields are set, false otherwise.
 		 */
-		public ProvenanceAction build() {
-			if (	// ew
+		public boolean isEmpty() {
+			return
 					time == null &&
 					caller == null &&
 					service == null &&
@@ -723,7 +722,15 @@ public ProvenanceAction build() {
 					externalData == null &&
 					subActions == null &&
 					custom == null &&
-					description == null) {
+					description == null;
+		}
+		
+		/** Build the {@link ProvenanceAction}. At least one field must be set before the build
+		 * attempt.
+		 * @return the provenance action.
+		 */
+		public ProvenanceAction build() {
+			if (isEmpty()) {
 				throw new IllegalArgumentException(
 						"At least one field in a provenance action must be provided");
 			}

src/us/kbase/workspace/ProvenanceAction.java

@@ -118,7 +118,7 @@ public static Provenance processProvenance(
 				checkAddlArgs(a.getAdditionalProperties(), a.getClass());
 				final Instant d = chooseInstant(a.getTime(), a.getEpoch(),
 						"Cannot specify both time and epoch in provenance action");
-				p.withAction(ProvenanceAction.getBuilder()
+				final ProvenanceAction.Builder pa = ProvenanceAction.getBuilder()
 						.withTime(d)
 						.withCaller(a.getCaller())
 						.withServiceName(a.getService())
@@ -135,9 +135,10 @@ public static Provenance processProvenance(
 						.withExternalData(processExternalData(a.getExternalData()))
 						.withSubActions(processSubActions(a.getSubactions()))
 						.withCustom(a.getCustom())
-						.withDescription(a.getDescription())
-						.build()
-				);
+						.withDescription(a.getDescription());
+				if (!pa.isEmpty()) { // requiring non-empty PAs broke external code unfortunately
+					p.withAction(pa.build());
+				}
 			} catch (IllegalArgumentException | NullPointerException e) {
 				throw new IllegalArgumentException(String.format("Provenance action #%s: %s",
 						li.nextIndex(), e.getLocalizedMessage()), e);

src/us/kbase/workspace/WorkspaceServer.java

@@ -56,11 +56,13 @@
 import us.kbase.workspace.database.mongo.exceptions.BlobStoreCommunicationException;
 import us.kbase.workspace.kbase.KBaseWorkspaceConfig.ListenerConfig;
 import us.kbase.workspace.kbase.BytestreamIdHandlerFactory.BytestreamClientCloner;
+import us.kbase.workspace.kbase.admin.AdministrationCommandSetInstaller;
 import us.kbase.workspace.kbase.admin.AdministratorHandler;
 import us.kbase.workspace.kbase.admin.AdministratorHandlerException;
 import us.kbase.workspace.kbase.admin.DefaultAdminHandler;
 import us.kbase.workspace.kbase.admin.KBaseAuth2AdminHandler;
 import us.kbase.workspace.kbase.admin.WorkspaceAdministration;
+import us.kbase.workspace.kbase.admin.WorkspaceAdministration.UserValidator;
 import us.kbase.workspace.listener.ListenerInitializationException;
 import us.kbase.workspace.listener.WorkspaceEventListener;
 import us.kbase.workspace.listener.WorkspaceEventListenerFactory;
@@ -78,9 +80,6 @@ public class InitWorkspaceServer {
 
 	public static final String COL_S3_OBJECTS = "s3_objects";
 
-	private static final int ADMIN_CACHE_MAX_SIZE = 100; // seems like more than enough admins
-	private static final int ADMIN_CACHE_EXP_TIME_MS = 5 * 60 * 1000; // cache admin role for 5m
-	
 	private static int maxUniqueIdCountPerCall = 100000;
 
 	private static int instanceCount = 0;
@@ -105,27 +104,20 @@ public boolean isFailed() {
 	}
 
 	public static class WorkspaceInitResults {
-		private final Workspace ws;
 		private final WorkspaceServerMethods wsmeth;
 		private final WorkspaceAdministration wsadmin;
-		private final Types types;
+		private final TypeServerMethods types;
 
 		public WorkspaceInitResults(
-				final Workspace ws,
 				final WorkspaceServerMethods wsmeth,
 				final WorkspaceAdministration wsadmin,
-				final Types types) {
+				final TypeServerMethods types) {
 			super();
-			this.ws = ws;
 			this.wsmeth = wsmeth;
 			this.wsadmin = wsadmin;
 			this.types = types;
 		}
 
-		public Workspace getWs() {
-			return ws;
-		}
-
 		public WorkspaceServerMethods getWsmeth() {
 			return wsmeth;
 		}
@@ -134,7 +126,7 @@ public WorkspaceAdministration getWsAdmin() {
 			return wsadmin;
 		}
 
-		public Types getTypes() {
+		public TypeServerMethods getTypes() {
 			return types;
 		}
 	}
@@ -189,23 +181,25 @@ public static WorkspaceInitResults initWorkspaceServer(
 			return null;
 		}
 		rep.reportInfo(String.format("Initialized %s backend", cfg.getBackendType().name()));
-		final Types types = new Types(wsdeps.typeDB);
+		// TODO CODE maybe merge these 2 classes?
+		final LocalTypeServerMethods types = new LocalTypeServerMethods(new Types(wsdeps.typeDB));
 		final IdReferenceHandlerSetFactoryBuilder builder = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(maxUniqueIdCountPerCall)
 				.withFactory(new HandleIdHandlerFactory(hsc))
 				.withFactory(wsdeps.shockFac)
 				.withFactory(wsdeps.sampleFac)
 				.build();
-		WorkspaceServerMethods wsmeth = new WorkspaceServerMethods(ws, types, builder, auth);
-		WorkspaceAdministration wsadmin = new WorkspaceAdministration(
-				ws, wsmeth, types, ah, ADMIN_CACHE_MAX_SIZE, ADMIN_CACHE_EXP_TIME_MS);
+		final WorkspaceServerMethods wsmeth = new WorkspaceServerMethods(ws, builder, auth);
+		final UserValidator userVal = (user, token) -> wsmeth.validateUser(user, token);
+		final WorkspaceAdministration wsadmin = AdministrationCommandSetInstaller.install(
+				WorkspaceAdministration.getBuilder(ah, userVal), wsmeth, types).build();
 		final String mem = String.format(
 				"Started workspace server instance %s. Free mem: %s Total mem: %s, Max mem: %s",
 				++instanceCount, Runtime.getRuntime().freeMemory(),
 				Runtime.getRuntime().totalMemory(),
 				Runtime.getRuntime().maxMemory());
 		rep.reportInfo(mem);
-		return new WorkspaceInitResults(ws, wsmeth, wsadmin, types);
+		return new WorkspaceInitResults(wsmeth, wsadmin, types);
 	}
 
 	private static AdministratorHandler getAdminHandler(