Clean up top level provenance class

Add a builder, make immutable

performanceanddevelopment/legacy/performance/GetObjectsLibSpeedTest.java

@@ -1,5 +1,7 @@
 package legacy.performance;
 
+import static us.kbase.workspace.test.WorkspaceTestCommon.basicProv;
+
 import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.OutputStreamWriter;
@@ -36,7 +38,6 @@
 import us.kbase.workspace.database.ByteArrayFileCacheManager.ByteArrayFileCache;
 import us.kbase.workspace.database.ObjectIDNoWSNoVer;
 import us.kbase.workspace.database.ObjectIdentifier;
-import us.kbase.workspace.database.Provenance;
 import us.kbase.workspace.database.ResourceUsageConfigurationBuilder;
 import us.kbase.workspace.database.Types;
 import us.kbase.workspace.database.Workspace;
@@ -106,7 +107,7 @@ public static void main(String[] args) throws Exception {
 				new WorkspaceSaveObject(//added obj name when autonaming removed
 						new ObjectIDNoWSNoVer(UUID.randomUUID().toString()
 								.replace("-", "")),
-						o, td, null, new Provenance(user), false)), fac);
+						o, td, null, basicProv(user), false)), fac);
 		o = null;
 
 		ObjectIdentifier oi = ObjectIdentifier.getBuilder(wsi).withName("auto1").build(); 

performanceanddevelopment/legacy/performance/us/kbase/workspace/performance/refsearch/GetReferencedObjectWithBFS.java

@@ -1,5 +1,7 @@
 package legacy.performance.us.kbase.workspace.performance.refsearch;
 
+import static us.kbase.workspace.test.WorkspaceTestCommon.basicProv;
+
 import java.io.File;
 import java.nio.file.Paths;
 import java.util.Arrays;
@@ -26,7 +28,6 @@
 import us.kbase.workspace.database.ObjectIDNoWSNoVer;
 import us.kbase.workspace.database.ObjectIdentifier;
 import us.kbase.workspace.database.ObjectInformation;
-import us.kbase.workspace.database.Provenance;
 import us.kbase.workspace.database.ResourceUsageConfigurationBuilder;
 import us.kbase.workspace.database.Types;
 import us.kbase.workspace.database.Workspace;
@@ -35,6 +36,7 @@
 import us.kbase.workspace.database.WorkspaceUser;
 import us.kbase.workspace.database.mongo.GridFSBlobStore;
 import us.kbase.workspace.database.mongo.MongoWorkspaceDB;
+import us.kbase.workspace.database.provenance.Provenance;
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
 
@@ -147,7 +149,7 @@ private static void runBranchedReferencesTest() throws Exception {
 		WorkspaceUser u2 = new WorkspaceUser("brcu2");
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(10).build().getFactory(null);
-		Provenance p = new Provenance(u1);
+		final Provenance p = basicProv(u1);
 		WorkspaceIdentifier read = new WorkspaceIdentifier("brcread");
 		WorkspaceIdentifier priv = new WorkspaceIdentifier("brcpriv");
 		for (int breadth = 1; breadth <= MAX_TREE_BREADTH; breadth++) {
@@ -184,7 +186,7 @@ private static List<ObjectInformation> generateReferences(
 			throws Exception {
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(100000).build().getFactory(null);
-		Provenance p = new Provenance(user);
+		final Provenance p = basicProv(user);
 		List<WorkspaceSaveObject> objs = new LinkedList<WorkspaceSaveObject>();
 		for (ObjectInformation oi: increfs) {
 			String ref = oi.getWorkspaceId() + "/" + oi.getObjectId() + "/" + oi.getVersion();
@@ -217,7 +219,7 @@ private static void runLinearReferencesTest() throws Exception {
 
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(10000).build().getFactory(null);
-		Provenance p = new Provenance(u1);
+		final Provenance p = basicProv(u1);
 		ObjectInformation o = WS.saveObjects(u1, priv, Arrays.asList(
 				new WorkspaceSaveObject(getRandomName(), new HashMap<String, String>(), LEAF_TYPE,
 						null, p, false)), fac).get(0);
@@ -250,7 +252,7 @@ private static ObjectInformation saveRefData(
 		refdata.put("refs", Arrays.asList(ref));
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(10000).build().getFactory(null);
-		Provenance p = new Provenance(u1);
+		final Provenance p = basicProv(u1);
 		return WS.saveObjects(u1, priv, Arrays.asList(
 				new WorkspaceSaveObject(getRandomName(), refdata, REF_TYPE, null, p, false)), fac)
 				.get(0);

performanceanddevelopment/legacy/performance/us/kbase/workspace/performance/refsearch/v0_3_5/GetReferencedObjectWithBFS.java

@@ -1,5 +1,7 @@
 package legacy.performance.us.kbase.workspace.performance.refsearch.v0_3_5; // note package changed from orig
 
+import static us.kbase.workspace.test.WorkspaceTestCommon.basicProv;
+
 import java.io.File;
 import java.nio.file.Paths;
 import java.util.Arrays;
@@ -17,23 +19,16 @@
 import us.kbase.typedobj.core.AbsoluteTypeDefId;
 import us.kbase.typedobj.core.TempFilesManager;
 import us.kbase.typedobj.core.TypeDefName;
-//import us.kbase.typedobj.core.TypedObjectValidator;
-//import us.kbase.typedobj.db.MongoTypeStorage;
-//import us.kbase.typedobj.db.TypeDefinitionDB;
 import us.kbase.typedobj.idref.IdReferenceHandlerSetFactory;
 import us.kbase.typedobj.idref.IdReferenceHandlerSetFactoryBuilder;
-//import us.kbase.workspace.database.DefaultReferenceParser;
 import us.kbase.workspace.database.ObjectIDNoWSNoVer;
 import us.kbase.workspace.database.ObjectIdentifier;
 import us.kbase.workspace.database.ObjectInformation;
-import us.kbase.workspace.database.Provenance;
-//import us.kbase.workspace.database.ResourceUsageConfigurationBuilder;
 import us.kbase.workspace.database.Workspace;
 import us.kbase.workspace.database.WorkspaceIdentifier;
 import us.kbase.workspace.database.WorkspaceSaveObject;
 import us.kbase.workspace.database.WorkspaceUser;
-//import us.kbase.workspace.database.mongo.GridFSBlobStore;
-//import us.kbase.workspace.database.mongo.MongoWorkspaceDB;
+import us.kbase.workspace.database.provenance.Provenance;
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
 
@@ -155,7 +150,7 @@ private static void runBranchedReferencesTest() throws Exception {
 		WorkspaceUser u2 = new WorkspaceUser("brcu2");
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(10).build().getFactory(null);
-		Provenance p = new Provenance(u1);
+		final Provenance p = basicProv(u1);
 		WorkspaceIdentifier read = new WorkspaceIdentifier("brcread");
 		WorkspaceIdentifier priv = new WorkspaceIdentifier("brcpriv");
 		for (int breadth = 1; breadth <= 10; breadth++) {
@@ -194,7 +189,7 @@ private static List<ObjectInformation> generateReferences(
 			throws Exception {
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(100000).build().getFactory(null);
-		Provenance p = new Provenance(user);
+		final Provenance p = basicProv(user);
 		List<WorkspaceSaveObject> objs = new LinkedList<WorkspaceSaveObject>();
 		for (ObjectInformation oi: increfs) {
 			String ref = oi.getWorkspaceId() + "/" + oi.getObjectId() + "/" + oi.getVersion();
@@ -228,7 +223,7 @@ private static void runLinearReferencesTest() throws Exception {
 
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(10000).build().getFactory(null);
-		Provenance p = new Provenance(u1);
+		final Provenance p = basicProv(u1);
 		ObjectInformation o = WS.saveObjects(u1, priv, Arrays.asList(
 				new WorkspaceSaveObject(getRandomName(), new HashMap<String, String>(), LEAF_TYPE,
 						null, p, false)), fac).get(0);
@@ -261,7 +256,7 @@ private static ObjectInformation saveRefData(
 		refdata.put("refs", Arrays.asList(ref));
 		final IdReferenceHandlerSetFactory fac = IdReferenceHandlerSetFactoryBuilder
 				.getBuilder(10000).build().getFactory(null);
-		Provenance p = new Provenance(u1);
+		final Provenance p = basicProv(u1);
 		return WS.saveObjects(u1, priv, Arrays.asList(
 				new WorkspaceSaveObject(getRandomName(), refdata, REF_TYPE, null, p, false)), fac)
 				.get(0);

src/us/kbase/common/test/TestCommon.java

@@ -283,6 +283,10 @@ public static Instant inst(final long epoch) {
 		return Instant.ofEpochMilli(epoch);
 	}
 
+	public static Instant now() {
+		return Instant.now();
+	}
+
 	public static final Optional<String> ES = Optional.empty();
 	public static final Optional<Long> EL = Optional.empty();
 	public static final Optional<Integer> EI = Optional.empty();

src/us/kbase/workspace/database/ResolvedSaveObject.java

@@ -8,6 +8,7 @@
 import us.kbase.typedobj.idref.IdReferenceType;
 import us.kbase.typedobj.idref.RemappedId;
 import us.kbase.workspace.database.WorkspaceUserMetadata.MetadataException;
+import us.kbase.workspace.database.provenance.Provenance;
 
 public class ResolvedSaveObject {
 

src/us/kbase/workspace/database/Workspace.java

@@ -725,7 +725,6 @@ public List<ObjectInformation> saveObjects(
 		int objcount = 1;
 		for (WorkspaceSaveObject wo: objects) {
 			//maintain ordering
-			wo.getProvenance().setWorkspaceID(Long.valueOf(rwsi.getID()));
 			final List<Reference> provrefs = new LinkedList<Reference>();
 			for (final ProvenanceAction action: wo.getProvenance().getActions()) {
 				for (final String ref: action.getWorkspaceObjects()) {
@@ -751,7 +750,7 @@ public List<ObjectInformation> saveObjects(
 			}
 
 			final ValidatedTypedObject rep = reports.get(wo);
-			saveobjs.add(wo.resolve(rep, refs, provrefs, extractedIDs));
+			saveobjs.add(wo.resolve(rwsi, rep, refs, provrefs, extractedIDs));
 			ttlObjSize += rep.calculateRelabeledSize();
 			if (rep.getRelabeledSize() > rescfg.getMaxObjectSize()) {
 				throw new IllegalArgumentException(String.format(

src/us/kbase/workspace/database/WorkspaceObjectData.java

@@ -13,6 +13,7 @@
 import us.kbase.typedobj.core.SubsetSelection;
 import us.kbase.typedobj.idref.IdReferenceType;
 import us.kbase.workspace.database.ByteArrayFileCacheManager.ByteArrayFileCache;
+import us.kbase.workspace.database.provenance.Provenance;
 
 /** A package containing (optionally) a workspace object's data along with provenance and
  * information about the object.

src/us/kbase/workspace/database/WorkspaceSaveObject.java

@@ -9,9 +9,17 @@
 import us.kbase.typedobj.core.ValidatedTypedObject;
 import us.kbase.typedobj.idref.IdReferenceType;
 import us.kbase.typedobj.idref.RemappedId;
+import us.kbase.workspace.database.provenance.Provenance;
 
 public class WorkspaceSaveObject {
 
+	// TODO TEST unit tests
+	// TODO JAVADOC
+
+	// Unfortunately UObjects aren't necessarily immutable so there's no way to make this truly
+	// immutable - although maybe could check that the UObject wraps a JsonTokenStream in which
+	// case it should be immutable (double check)
+
 	private final ObjectIDNoWSNoVer id;
 	private final UObject data;
 	private final TypeDefId type;
@@ -69,13 +77,20 @@ public boolean isHidden() {
 
 	// provrefs *must* be in the same ordering as they are in the provenance actions
 	public ResolvedSaveObject resolve(
+			final ResolvedWorkspaceID wsid,
 			final ValidatedTypedObject rep,
 			final Set<Reference> references,
 			final List<Reference> provenancerefs,
 			final Map<IdReferenceType, Set<RemappedId>> extractedIDs) {
-		return new ResolvedSaveObject(this.id, this.userMeta,
-				this.provenance, this.hidden, rep, references,
-				provenancerefs, extractedIDs);
+		return new ResolvedSaveObject(
+				this.id,
+				this.userMeta,
+				this.provenance.updateWorkspaceID(wsid.getID()),
+				this.hidden,
+				rep,
+				references,
+				provenancerefs,
+				extractedIDs);
 	}
 
 	@Override

src/us/kbase/workspace/database/mongo/MongoWorkspaceDB.java

@@ -72,7 +72,7 @@
 import us.kbase.workspace.database.Permission;
 import us.kbase.workspace.database.PermissionSet;
 import us.kbase.workspace.database.PermissionSet.Builder;
-import us.kbase.workspace.database.Provenance;
+import us.kbase.workspace.database.provenance.Provenance;
 import us.kbase.workspace.database.Reference;
 import us.kbase.workspace.database.ResolvedObjectID;
 import us.kbase.workspace.database.ResolvedObjectIDNoVer;
@@ -2013,8 +2013,14 @@ private Map<String, String> emptyToNull(final Map<String, String> map) {
 	private Map<String, Object> toDocument(final Provenance p) {
 		final Map<String, Object> ret = new HashMap<>();
 		ret.put(Fields.PROV_USER, p.getUser().getUser());
-		ret.put(Fields.PROV_DATE, p.getDate());
-		ret.put(Fields.PROV_WS_ID, p.getWorkspaceID());
+		// this is a bit of a hack, but the JSON representation of an Instant is ~30 chars bigger
+		// than a Date and not always the same length, which screws with the size calculations in
+		// tests when writing this map to JSON (which is also a bit of a hack, but doesn't need to
+		// be byte level accurate). Both instants and dates are accepted by Mongo so just use a
+		// Date here.
+		// Might make more sense to write BSON vs. JSON for the size calcs.
+		ret.put(Fields.PROV_DATE, Date.from(p.getDate()));
+		ret.put(Fields.PROV_WS_ID, p.getWorkspaceID().orElse(null));
 		final List<Map<String, Object>> actions = new LinkedList<>();
 		ret.put(Fields.PROV_ACTIONS, actions);
 		for (final ProvenanceAction pa: p.getActions()) {
@@ -2032,7 +2038,7 @@ private Map<String, Object> toDocument(final Provenance p) {
 			paret.put(Fields.PROV_ACTION_SCRIPT_VER, pa.getScriptVersion().orElse(null));
 			paret.put(Fields.PROV_ACTION_SERVICE, pa.getServiceName().orElse(null));
 			paret.put(Fields.PROV_ACTION_SERVICE_VER, pa.getServiceVersion().orElse(null));
-			paret.put(Fields.PROV_ACTION_TIME, pa.getTime().orElse(null));
+			paret.put(Fields.PROV_ACTION_TIME, pa.getTime().map(t -> Date.from(t)).orElse(null));
 			paret.put(Fields.PROV_ACTION_WS_OBJS, emptyToNull(pa.getWorkspaceObjects()));
 
 			final List<Map<String, Object>> extdata = new LinkedList<>();
@@ -2745,11 +2751,11 @@ private Provenance toProvenance(
 			final List<String> resolvedRefs) {
 		// make a copy we can mutate
 		final List<String> rrcopy = new LinkedList<>(resolvedRefs);
-		final Provenance ret = new Provenance(
+		final Provenance.Builder ret = Provenance.getBuilder(
 				new WorkspaceUser(p.getString(Fields.PROV_USER)),
-				p.getDate(Fields.PROV_DATE));
-		// objects saved before version 0.4.1 will have null workspace IDs
-		ret.setWorkspaceID(p.getLong(Fields.PROV_WS_ID));
+				p.getDate(Fields.PROV_DATE).toInstant())
+				// objects saved before version 0.4.1 will have null workspace IDs
+				.withWorkspaceID(p.getLong(Fields.PROV_WS_ID));
 		for (final Document pa: p.getList(Fields.PROV_ACTIONS, Document.class)) {
 			@SuppressWarnings("unchecked")
 			final Map<String, String> precustom =
@@ -2764,7 +2770,7 @@ private Provenance toProvenance(
 			final List<String> actionRefs = new LinkedList<>(rrcopy.subList(0, refcnt));
 			rrcopy.subList(0, refcnt).clear();
 
-			ret.addAction(ProvenanceAction.getBuilder()
+			ret.withAction(ProvenanceAction.getBuilder()
 					.withExternalData(toExternalData(pa.getList(
 							Fields.PROV_ACTION_EXTERNAL_DATA, Document.class)))
 					.withSubActions(toSubAction(pa.getList(
@@ -2787,7 +2793,7 @@ private Provenance toProvenance(
 					.build()
 					);
 		}
-		return ret;
+		return ret.build();
 	}
 
 	private List<Object> getParamList(final Document provaction) {

src/us/kbase/workspace/database/provenance/Common.java

@@ -78,4 +78,8 @@ static <T> List<T> immutable(final List<T> list) {
 		 */
 		return Collections.unmodifiableList(new ArrayList<>(list));
 	}
+
+	static <T> List<T> getList(final List<T> list) {
+		return list == null ? Collections.emptyList() : list;
+	}
 }