towards #52 and globalbioticinteractions/globalbioticinteractions#1030

globalbioticinteractions · Dec 18, 2024 · c008712 · c008712
1 parent 4e14a2d
commit c008712
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Showing 12 changed files with 45 additions and 48 deletions.
diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUpdate.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUpdate.java
@@ -68,12 +68,12 @@ protected void doRun() {
                     new ActivityListener() {
 
                         @Override
-                        public void onStarted(IRI parentActivityId, UUID activityId, IRI request) {
+                        public void onStarted(IRI parentActivityId, IRI activityId, IRI request) {
 
                         }
 
                         @Override
-                        public void onCompleted(IRI parentActivityId, UUID activityId, IRI request, IRI response, URI localPathOfResponseData) {
+                        public void onCompleted(IRI parentActivityId, IRI activityId, IRI request, IRI response, URI localPathOfResponseData) {
 
                         }
                     }

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUtil.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUtil.java
@@ -1,5 +1,6 @@
 package org.globalbioticinteractions.elton.cmd;
 
+import bio.guoda.preston.RefNodeFactory;
 import bio.guoda.preston.cmd.ActivityContext;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.rdf.api.IRI;
@@ -114,10 +115,10 @@ public String getDescription() {
                             return null;
                         }
                     },
-                    new Supplier<UUID>() {
+                    new Supplier<IRI>() {
                         @Override
-                        public UUID get() {
-                            return UUID.randomUUID();
+                        public IRI get() {
+                            return RefNodeFactory.toIRI(UUID.randomUUID());
                         }
                     });
 

diff --git a/src/main/java/org/globalbioticinteractions/elton/store/AccessLogger.java b/src/main/java/org/globalbioticinteractions/elton/store/AccessLogger.java
@@ -22,12 +22,12 @@ public AccessLogger(String namespace, String provDir) {
     }
 
     @Override
-    public void onStarted(IRI parentActivityId, UUID activityId, IRI request) {
+    public void onStarted(IRI parentActivityId, IRI activityId, IRI request) {
 
     }
 
     @Override
-    public void onCompleted(IRI parentActivityId, UUID activityId, IRI request, IRI response, URI localPathOfResponseData) {
+    public void onCompleted(IRI parentActivityId, IRI activityId, IRI request, IRI response, URI localPathOfResponseData) {
         try {
             ContentProvenance contentProvenanceWithNamespace
                     = new ContentProvenance(this.namespace,

diff --git a/src/main/java/org/globalbioticinteractions/elton/store/ActivityListener.java b/src/main/java/org/globalbioticinteractions/elton/store/ActivityListener.java
@@ -3,19 +3,18 @@
 import org.apache.commons.rdf.api.IRI;
 
 import java.net.URI;
-import java.util.UUID;
 
 public interface ActivityListener {
 
     void onStarted(
             IRI parentActivityId,
-            UUID activityId,
+            IRI activityId,
             IRI request
     );
 
     void onCompleted(
             IRI parentActivityId,
-            UUID activityId,
+            IRI activityId,
             IRI request,
             IRI response,
             URI localPathOfResponseData

diff --git a/src/main/java/org/globalbioticinteractions/elton/store/ActivityProxy.java b/src/main/java/org/globalbioticinteractions/elton/store/ActivityProxy.java
@@ -14,12 +14,12 @@ public ActivityProxy(List<ActivityListener> listeners) {
     }
 
     @Override
-    public void onStarted(IRI parentActivityId, UUID activityId, IRI request) {
+    public void onStarted(IRI parentActivityId, IRI activityId, IRI request) {
 
     }
 
     @Override
-    public void onCompleted(IRI parentActivityId, UUID activityId, IRI request, IRI response, URI localPathOfResponseData) {
+    public void onCompleted(IRI parentActivityId, IRI activityId, IRI request, IRI response, URI localPathOfResponseData) {
         listeners.forEach(l -> l.onCompleted(parentActivityId, activityId, request, response, localPathOfResponseData));
     }
 

diff --git a/src/main/java/org/globalbioticinteractions/elton/store/CachePullThroughPrestonStore.java b/src/main/java/org/globalbioticinteractions/elton/store/CachePullThroughPrestonStore.java
@@ -18,7 +18,6 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URI;
-import java.util.UUID;
 import java.util.function.Supplier;
 
 public class CachePullThroughPrestonStore extends CachePullThrough {
@@ -27,7 +26,7 @@ public class CachePullThroughPrestonStore extends CachePullThrough {
     private final ResourceService resourceService;
     private final String dataDir;
     private final ActivityContext ctx;
-    private final Supplier<UUID> uuidFactory;
+    private final Supplier<IRI> iriFactory;
 
     private ActivityListener dereferenceListener;
 
@@ -38,7 +37,7 @@ public CachePullThroughPrestonStore(String namespace,
                                         String provDir,
                                         ActivityListener dereferenceListener,
                                         ActivityContext ctx,
-                                        Supplier<UUID> uuidFactory) {
+                                        Supplier<IRI> iriFactory) {
         super(namespace,
                 resourceServiceLocal,
                 contentPathFactory,
@@ -50,7 +49,7 @@ public CachePullThroughPrestonStore(String namespace,
         this.resourceService = resourceServiceLocal;
         this.dereferenceListener = dereferenceListener;
         this.ctx = ctx;
-        this.uuidFactory = uuidFactory;
+        this.iriFactory = iriFactory;
     }
 
     @Override
@@ -76,7 +75,7 @@ public InputStream retrieve(URI resourceURI) throws IOException {
         try {
             IRI request = RefNodeFactory.toIRI(resourceURI);
             IRI parentActivityId = ctx.getActivity();
-            UUID activityId = uuidFactory.get();
+            IRI activityId = iriFactory.get();
 
             dereferenceListener.onStarted(
                     parentActivityId,

diff --git a/src/main/java/org/globalbioticinteractions/elton/store/ProvLogger.java b/src/main/java/org/globalbioticinteractions/elton/store/ProvLogger.java
@@ -20,12 +20,12 @@ public ProvLogger(StatementListener listener) {
     }
 
     @Override
-    public void onStarted(IRI parentActivityId, UUID activityId, IRI request) {
+    public void onStarted(IRI parentActivityId, IRI activityId, IRI request) {
 
     }
 
     @Override
-    public void onCompleted(IRI parentActivityId, UUID activityId, IRI request, IRI response, URI localPathOfResponseData) {
+    public void onCompleted(IRI parentActivityId, IRI activityId, IRI request, IRI response, URI localPathOfResponseData) {
         if (listener != null) {
             ActivityUtil.emitDownloadActivity(
                     request,
@@ -36,7 +36,7 @@ public void emit(Quad quad) {
                             listener.on(quad);
                         }
                     },
-                    Optional.of(RefNodeFactory.toIRI(activityId))
+                    Optional.of(activityId)
             );
         }
     }

diff --git a/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistrySingleDir.java b/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistrySingleDir.java
@@ -1,5 +1,6 @@
 package org.globalbioticinteractions.elton.util;
 
+import bio.guoda.preston.RefNodeFactory;
 import bio.guoda.preston.cmd.ActivityContext;
 import org.apache.commons.rdf.api.IRI;
 import org.eol.globi.service.ResourceService;
@@ -78,10 +79,10 @@ public String getDescription() {
                                 return null;
                             }
                         },
-                        new Supplier<UUID>() {
+                        new Supplier<IRI>() {
                             @Override
-                            public UUID get() {
-                                return UUID.randomUUID();
+                            public IRI get() {
+                                return RefNodeFactory.toIRI(UUID.randomUUID());
                             }
                         }
                 )

diff --git a/src/test/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImplTest.java b/src/test/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImplTest.java
@@ -1,8 +1,8 @@
 package org.globalbioticinteractions.elton.cmd;
 
 import org.apache.commons.rdf.api.IRI;
-import org.globalbioticinteractions.dataset.DatasetRegistryException;
 import org.globalbioticinteractions.dataset.DatasetRegistry;
+import org.globalbioticinteractions.dataset.DatasetRegistryException;
 import org.globalbioticinteractions.elton.store.ActivityListener;
 import org.hamcrest.core.Is;
 import org.junit.Test;
@@ -11,7 +11,6 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
-import java.util.UUID;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 
@@ -30,12 +29,12 @@ public void list() throws DatasetRegistryException {
                     new ActivityListener() {
 
                         @Override
-                        public void onStarted(IRI parentActivityId, UUID activityId, IRI request) {
+                        public void onStarted(IRI parentActivityId, IRI activityId, IRI request) {
 
                         }
 
                         @Override
-                        public void onCompleted(IRI parentActivityId, UUID activityId, IRI request, IRI response, URI localPathOfResponseData) {
+                        public void onCompleted(IRI parentActivityId, IRI activityId, IRI request, IRI response, URI localPathOfResponseData) {
 
                         }
                     }).createRegistryByName(supportedRegistry);

diff --git a/src/test/java/org/globalbioticinteractions/elton/store/AccessLoggerTest.java b/src/test/java/org/globalbioticinteractions/elton/store/AccessLoggerTest.java
@@ -30,7 +30,7 @@ public void testCreatProvDirIfNotExists() throws IOException {
         String namespace = "some/namespace";
         new AccessLogger(namespace, provDir).onCompleted(
                 RefNodeFactory.toIRI(UUID.randomUUID()),
-                UUID.randomUUID(),
+                RefNodeFactory.toIRI(UUID.randomUUID()),
                 RefNodeFactory.toIRI("some:request"),
                 RefNodeFactory.toIRI("some:response"),
                 URI.create("foo/bar")

diff --git a/src/test/java/org/globalbioticinteractions/elton/store/ActivityListenerImpl.java b/src/test/java/org/globalbioticinteractions/elton/store/ActivityListenerImpl.java
@@ -31,22 +31,20 @@ public Literal get() {
     }
 
     @Override
-    public void onStarted(IRI parentActivitiyId, UUID activityId, IRI request) {
-        IRI downloadActivity = RefNodeFactory.toIRI(activityId);
-        listener.on(RefNodeFactory.toStatement(downloadActivity, downloadActivity, RefNodeConstants.IS_A, RefNodeConstants.GENERATION));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, downloadActivity, RefNodeConstants.WAS_INFORMED_BY, parentActivitiyId));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, downloadActivity, RefNodeConstants.STARTED_AT_TIME, clock.get()));
+    public void onStarted(IRI parentActivitiyId, IRI activityId, IRI request) {
+        listener.on(RefNodeFactory.toStatement(activityId, activityId, RefNodeConstants.IS_A, RefNodeConstants.GENERATION));
+        listener.on(RefNodeFactory.toStatement(activityId, activityId, RefNodeConstants.WAS_INFORMED_BY, parentActivitiyId));
+        listener.on(RefNodeFactory.toStatement(activityId, activityId, RefNodeConstants.STARTED_AT_TIME, clock.get()));
     }
 
     @Override
-    public void onCompleted(IRI parentActivityId, UUID activityId, IRI request, IRI response, URI localPathOfResponseData) {
-        BlankNodeOrIRI downloadActivity = RefNodeFactory.toIRI(activityId);
-        listener.on(RefNodeFactory.toStatement(downloadActivity, response, RefNodeConstants.WAS_GENERATED_BY, downloadActivity));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, response, RefNodeConstants.QUALIFIED_GENERATION, downloadActivity));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, downloadActivity, RefNodeConstants.GENERATED_AT_TIME, clock.get()));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, downloadActivity, RefNodeConstants.IS_A, RefNodeConstants.GENERATION));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, downloadActivity, RefNodeConstants.USED, request));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, request, RefNodeConstants.HAS_VERSION, response));
-        listener.on(RefNodeFactory.toStatement(downloadActivity, downloadActivity, RefNodeConstants.ENDED_AT_TIME, clock.get()));
+    public void onCompleted(IRI parentActivityId, IRI activityId, IRI request, IRI response, URI localPathOfResponseData) {
+        listener.on(RefNodeFactory.toStatement(activityId, response, RefNodeConstants.WAS_GENERATED_BY, activityId));
+        listener.on(RefNodeFactory.toStatement(activityId, response, RefNodeConstants.QUALIFIED_GENERATION, activityId));
+        listener.on(RefNodeFactory.toStatement(activityId, activityId, RefNodeConstants.GENERATED_AT_TIME, clock.get()));
+        listener.on(RefNodeFactory.toStatement(activityId, activityId, RefNodeConstants.IS_A, RefNodeConstants.GENERATION));
+        listener.on(RefNodeFactory.toStatement(activityId, activityId, RefNodeConstants.USED, request));
+        listener.on(RefNodeFactory.toStatement(activityId, request, RefNodeConstants.HAS_VERSION, response));
+        listener.on(RefNodeFactory.toStatement(activityId, activityId, RefNodeConstants.ENDED_AT_TIME, clock.get()));
     }
 }
diff --git a/src/test/java/org/globalbioticinteractions/elton/store/CachePullThroughPrestonStoreTest.java b/src/test/java/org/globalbioticinteractions/elton/store/CachePullThroughPrestonStoreTest.java
@@ -124,10 +124,10 @@ public IRI getActivity() {
             public String getDescription() {
                 return null;
             }
-        }, new Supplier<UUID>() {
+        }, new Supplier<IRI>() {
             @Override
-            public UUID get() {
-                return UUID.randomUUID();
+            public IRI get() {
+                return RefNodeFactory.toIRI(UUID.randomUUID());
             }
         }
         );
@@ -188,11 +188,11 @@ public String getDescription() {
             }
         };
 
-        Supplier<UUID> uuidFactory = new Supplier<UUID>() {
+        Supplier<IRI> uuidFactory = new Supplier<IRI>() {
 
             @Override
-            public UUID get() {
-                return UUID.fromString("e4fe8c5c-1455-46c6-bcfe-f11a065978aa");
+            public IRI get() {
+                return RefNodeFactory.toIRI(UUID.fromString("e4fe8c5c-1455-46c6-bcfe-f11a065978aa"));
             }
         };