Persistence refactor

.circleci/config.yml

@@ -32,13 +32,13 @@ jobs:
           command: |
             docker create -v /etc/newman --name mms_test_configs alpine:3.4 /bin/true
             docker cp example/. mms_test_configs:/etc/newman
-            docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run crud.postman_collection.json -e test-env.json --delay-request 500
+            docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run crud.postman_collection.json -e test-env.json --delay-request 1000
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run cameo.postman_collection.json -e test-env.json --delay-request 1000
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run jupyter.postman_collection.json -e test-env.json --delay-request 500
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run localauth.postman_collection.json -e test-env.json --delay-request 500
-            docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run permissions.postman_collection.json -e test-env.json --delay-request 500
+            docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run permissions.postman_collection.json -e test-env.json --delay-request 1000
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run search.postman_collection.json -e test-env.json --delay-request 1000
-            docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run artifacts.postman_collection.json -e test-env.json --delay-request 500
+            docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run artifacts.postman_collection.json -e test-env.json --delay-request 1000
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run elastic.postman_collection.json -e test-env.json --delay-request 500
             docker run --volumes-from mms_test_configs --network container:mms -t postman/newman run groups.postman_collection.json -e test-env.json --delay-request 500
 

artifacts/src/main/java/org/openmbee/mms/artifacts/crud/ArtifactsContext.java

@@ -0,0 +1,13 @@
+package org.openmbee.mms.artifacts.crud;
+
+public class ArtifactsContext {
+    private static ThreadLocal<Boolean> artifactContext = new ThreadLocal<>();
+
+    public static void setArtifactContext(Boolean isArtifactContext) {
+        artifactContext.set(isArtifactContext);
+    }
+
+    public static boolean isArtifactContext() {
+        return Boolean.TRUE.equals(artifactContext.get());
+    }
+}

artifacts/src/main/java/org/openmbee/mms/artifacts/crud/ArtifactsPersistenceNodeUpdateFilter.java

@@ -0,0 +1,24 @@
+package org.openmbee.mms.artifacts.crud;
+
+import org.openmbee.mms.artifacts.json.ArtifactJson;
+import org.openmbee.mms.core.services.NodeChangeInfo;
+import org.openmbee.mms.crud.domain.NodeUpdateFilter;
+import org.openmbee.mms.json.ElementJson;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ArtifactsPersistenceNodeUpdateFilter implements NodeUpdateFilter {
+    @Override
+    public boolean filterUpdate(NodeChangeInfo nodeChangeInfo, ElementJson updated, ElementJson existing) {
+        if(ArtifactsContext.isArtifactContext()) {
+            return true;
+        }
+        //Ensure artifacts aren't cleared or added by the regular element update process
+        if(existing.containsKey(ArtifactJson.ARTIFACTS)) {
+            updated.put(ArtifactJson.ARTIFACTS, existing.get(ArtifactJson.ARTIFACTS));
+        } else {
+            updated.remove(ArtifactJson.ARTIFACTS);
+        }
+        return true;
+    }
+}

artifacts/src/main/java/org/openmbee/mms/artifacts/pubsub/ArtifactsElementsHookSubscriber.java

@@ -22,9 +22,9 @@ public void acceptHook(Object payload) {
         ElementUpdateHook elementUpdateHook = (ElementUpdateHook) payload;
         if(elementUpdateHook.getElements() != null) {
             //Ignore any artifact changes coming in outside of the Artifacts Controller
-            elementUpdateHook.getElements().parallelStream().forEach(v -> {
-                v.remove(ArtifactJson.ARTIFACTS);
-            });
+            elementUpdateHook.getElements().parallelStream().forEach(v ->
+                v.remove(ArtifactJson.ARTIFACTS)
+            );
         }
     }
 }

artifacts/src/main/java/org/openmbee/mms/artifacts/service/DefaultArtifactService.java

@@ -1,19 +1,20 @@
 package org.openmbee.mms.artifacts.service;
 
+import org.openmbee.mms.artifacts.crud.ArtifactsContext;
 import org.openmbee.mms.artifacts.storage.ArtifactStorage;
 import org.openmbee.mms.artifacts.ArtifactConstants;
 import org.openmbee.mms.artifacts.objects.ArtifactResponse;
-import org.openmbee.mms.core.dao.ProjectDAO;
+import org.openmbee.mms.core.dao.ProjectPersistence;
 import org.openmbee.mms.core.exceptions.BadRequestException;
 import org.openmbee.mms.core.exceptions.ConflictException;
 import org.openmbee.mms.core.exceptions.NotFoundException;
 import org.openmbee.mms.core.objects.ElementsRequest;
 import org.openmbee.mms.core.objects.ElementsResponse;
 import org.openmbee.mms.core.services.NodeService;
 import org.openmbee.mms.crud.services.ServiceFactory;
-import org.openmbee.mms.data.domains.global.Project;
 import org.openmbee.mms.artifacts.json.ArtifactJson;
 import org.openmbee.mms.json.ElementJson;
+import org.openmbee.mms.json.ProjectJson;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.util.DigestUtils;
@@ -30,7 +31,7 @@ public class DefaultArtifactService implements ArtifactService {
 
     private ArtifactStorage artifactStorage;
     private ServiceFactory serviceFactory;
-    private ProjectDAO projectRepository;
+    private ProjectPersistence projectPersistence;
 
     @Autowired
     public void setArtifactStorage(ArtifactStorage artifactStorage) {
@@ -43,16 +44,19 @@ public void setServiceFactory(ServiceFactory serviceFactory) {
     }
 
     @Autowired
-    public void setProjectRepository(ProjectDAO projectRepository) {
-        this.projectRepository = projectRepository;
+    public void setProjectPersistence(ProjectPersistence projectPersistence) {
+        this.projectPersistence = projectPersistence;
     }
 
     @Override
     public ArtifactResponse get(String projectId, String refId, String id, Map<String, String> params) {
         NodeService nodeService = getNodeService(projectId);
         ElementJson elementJson = getElement(nodeService, projectId, refId, id, params);
-
-        ArtifactJson artifact = getExistingArtifact(ArtifactJson.getArtifacts(elementJson), params, elementJson);
+        List<ArtifactJson> artifacts = ArtifactJson.getArtifacts(elementJson);
+        ArtifactJson artifact = new ArtifactJson();
+        if (artifacts != null) {
+            artifact = getExistingArtifact(artifacts, params, elementJson);
+        }
         byte[] data = artifactStorage.get(artifact.getLocation(), elementJson, artifact.getMimeType());
         ArtifactResponse response = new ArtifactResponse();
         response.setData(data);
@@ -90,7 +94,12 @@ public ElementsResponse createOrUpdate(String projectId, String refId, String id
         elementJson = attachOrUpdateArtifact(elementJson, artifactLocation, fileExtension, mimeType, "internal", checksum);
         ElementsRequest elementsRequest = new ElementsRequest();
         elementsRequest.setElements(Arrays.asList(elementJson));
-        return nodeService.createOrUpdate(projectId, refId, elementsRequest, params, user);
+        try {
+            ArtifactsContext.setArtifactContext(true);
+            return nodeService.createOrUpdate(projectId, refId, elementsRequest, params, user);
+        } finally {
+            ArtifactsContext.setArtifactContext(false);
+        }
     }
 
     @Override
@@ -99,20 +108,28 @@ public ElementsResponse disassociate(String projectId, String refId, String id,
         ElementJson elementJson = getElement(nodeService, projectId, refId, id, params);
 
         List<ArtifactJson> artifacts = ArtifactJson.getArtifacts(elementJson);
+        if (artifacts == null) {
+            throw new NotFoundException("Artifacts not found");
+        } 
         ArtifactJson artifact = getExistingArtifact(artifacts, params, elementJson);
         artifacts.remove(artifact);
         ArtifactJson.setArtifacts(elementJson, artifacts);
         ElementsRequest elementsRequest = new ElementsRequest();
         elementsRequest.setElements(Arrays.asList(elementJson));
-        return nodeService.createOrUpdate(projectId, refId, elementsRequest, params, user);
+        try {
+            ArtifactsContext.setArtifactContext(true);
+            return nodeService.createOrUpdate(projectId, refId, elementsRequest, params, user);
+        } finally {
+            ArtifactsContext.setArtifactContext(false);
+        }
     }
 
     private ElementJson getElement(NodeService nodeService, String projectId, String refId, String id, Map<String, String> params) {
 
         ElementsResponse elementsResponse = nodeService.read(projectId, refId, id, params);
-        if(elementsResponse.getElements() == null || elementsResponse.getElements().isEmpty()) {
+        if (elementsResponse.getElements() == null || elementsResponse.getElements().isEmpty()) {
             throw new NotFoundException("Element not found");
-        } else if(elementsResponse.getElements().size() > 1) {
+        } else if (elementsResponse.getElements().size() > 1) {
             throw new ConflictException("Multiple elements found with id " + id);
         } else {
             return elementsResponse.getElements().get(0);
@@ -124,10 +141,18 @@ private ElementJson attachOrUpdateArtifact(ElementJson elementJson, String artif
         List<ArtifactJson> artifacts = ArtifactJson.getArtifacts(elementJson);
         ArtifactJson artifact;
         try {
-            artifact = getExistingArtifact(artifacts, mimeType, null, elementJson);
+            //nested try/nullcheck OK?
+            if (artifacts != null) {
+                artifact = getExistingArtifact(artifacts, mimeType, null, elementJson);
+            } else {
+                throw new NotFoundException("Null artifact exception");
+            }
+
         } catch(NotFoundException ex) {
             artifact = new ArtifactJson();
-            artifacts.add(artifact);
+            if (artifacts != null) {
+                artifacts.add(artifact);
+            }
         }
 
         artifact.setLocation(artifactLocation);
@@ -145,24 +170,24 @@ private ArtifactJson getExistingArtifact(List<ArtifactJson> artifacts, Map<Strin
     }
 
     private ArtifactJson getExistingArtifact(List<ArtifactJson> artifacts, String mimeType, String extension, ElementJson element) {
-        if(mimeType == null && extension == null) {
+        if (mimeType == null && extension == null) {
             throw new BadRequestException("Missing mimetype or extension");
         }
         //Element representation is unique by mimeType and extension
-        Optional<ArtifactJson> existing = artifacts.stream().filter(v -> {
-            return (mimeType != null && mimeType.equals(v.getMimeType())) || (extension != null && extension.equals(v.getExtension()));
-        }).findFirst();
-        if(existing.isPresent()) {
+        Optional<ArtifactJson> existing = artifacts.stream().filter(v ->
+            (mimeType != null && mimeType.equals(v.getMimeType())) || (extension != null && extension.equals(v.getExtension()))
+        ).findFirst();
+        if (existing.isPresent()) {
             return existing.get();
         }
         throw new NotFoundException(element);
     }
 
     private String getFileExtension(MultipartFile file) {
         String originalFilename = file.getOriginalFilename();
-        if(originalFilename != null) {
+        if (originalFilename != null) {
             int inx = originalFilename.lastIndexOf('.');
-            if(inx > 0) {
+            if (inx > 0) {
                 return originalFilename.substring(inx + 1);
             }
         }
@@ -191,8 +216,8 @@ private String getProjectType(String projectId) {
         return getProject(projectId).getProjectType();
     }
 
-    private Project getProject(String projectId) {
-        Optional<Project> p = projectRepository.findByProjectId(projectId);
+    private ProjectJson getProject(String projectId) {
+        Optional<ProjectJson> p = projectPersistence.findById(projectId);
         if (p.isPresent()) {
             return p.get();
         }

authenticator/authenticator.gradle

@@ -1,14 +1,19 @@
 dependencies {
-    implementation project(':rdb')
     api project(':core')
 
     api commonDependencies.'spring-security-web'
 
     implementation commonDependencies.'servlet-api'
-    implementation group: 'io.jsonwebtoken', name: 'jjwt-api', version: '0.10.5'
+    implementation commonDependencies.'jjwt-api'
 
-    runtimeOnly group: 'io.jsonwebtoken', name: 'jjwt-impl', version: '0.10.5'
-    runtimeOnly group: 'io.jsonwebtoken', name: 'jjwt-jackson', version: '0.10.5'
+    runtimeOnly commonDependencies.'jjwt-impl'
+    runtimeOnly commonDependencies.'jjwt-jackson'
 
     testImplementation commonDependencies.'spring-boot-starter-test'
 }
+
+tasks {
+    processResources {
+        duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+    }
+}

authenticator/src/main/java/org/openmbee/mms/authenticator/security/JwtTokenGenerator.java

@@ -101,7 +101,10 @@ private Date generateExpirationDate() {
 
     private boolean isTokenExpired(String token) {
         final Date expirationDate = getExpirationDateFromToken(token);
-        return expirationDate.before(new Date());
+        if (expirationDate != null) {
+            return expirationDate.before(new Date());
+        }
+        return true;
     }
 
     @Override

build.gradle

@@ -33,6 +33,9 @@ ext {
         'jackson-databind'              : "com.fasterxml.jackson.core:jackson-databind:$jacksonVersion",
         'jackson-datatype-hibernate5'   : "com.fasterxml.jackson.datatype:jackson-datatype-hibernate5:$jacksonVersion",
         'jackson-datatype-jsr310'       : "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:$jacksonVersion",
+        'jjwt-api'                      : "io.jsonwebtoken:jjwt-api:$jwtTokenVersion",
+        'jjwt-impl'                     : "io.jsonwebtoken:jjwt-impl:$jwtTokenVersion",
+        'jjwt-jackson'                  : "io.jsonwebtoken:jjwt-jackson:$jwtTokenVersion",
         'spring-boot-starter-test'      : 'org.springframework.boot:spring-boot-starter-test:2.2.4.RELEASE'
     ]
 }

cameo/cameo.gradle

@@ -1,5 +1,6 @@
 dependencies {
     implementation project(':crud')
+    implementation project(':view')
 
     testImplementation commonDependencies.'spring-boot-starter-test'
 }

cameo/src/main/java/org/openmbee/mms/cameo/CameoConstants.java

@@ -14,6 +14,7 @@ public class CameoConstants {
     public static final String CLASSIFIERIDS = "classifierIds";
     public static final String CLIENTDEPENDENCYIDS = "clientDependencyIds";
     public static final String COLLABORATIONUSEIDS = "collaborationUseIds";
+    public static final String COMMITID = "commitId";
     public static final String DATATYPEID = "datatypeId";
     public static final String DEFAULTVALUE = "defaultValue";
     public static final String DEFININGFEATUREID = "definingFeatureId";
@@ -46,12 +47,15 @@ public class CameoConstants {
     public static final String NAME = "name";
     public static final String NAMEEXPRESSION = "nameExpression";
     public static final String NAVIGABLEOWNEDENDIDS = "navigableOwnedEndIds";
+    public static final String NONE = "none";
     public static final String OWNEDATTRIBUTEIDS = "ownedAttributeIds";
     public static final String OWNEDENDIDS = "ownedEndIds";
     public static final String OWNERID = "ownerId";
     public static final String PACKAGEIMPORTIDS = "packageImportIds";
     public static final String PACKAGEMERGEIDS = "packageMergeIds";
+    public static final String PARENTID = "_parentId";
     public static final String POWERTYPEEXTENTIDS = "powertypeExtentIds";
+    public static final String PROPERTY = "Property";
     public static final String PROPERTYID = "propertyId";
     public static final String PROPERTYTYPE = "propertyType";
     public static final String PROFILEAPPLICATIONIDS = "profileApplicationIds";

cameo/src/main/java/org/openmbee/mms/cameo/services/CameoCommitService.java

@@ -1,9 +1,8 @@
 package org.openmbee.mms.cameo.services;
 
-import org.openmbee.mms.core.config.ContextHolder;
 import org.openmbee.mms.core.services.CommitService;
 import org.openmbee.mms.crud.services.DefaultCommitService;
-import org.openmbee.mms.data.domains.scoped.Commit;
+import org.openmbee.mms.json.CommitJson;
 import org.springframework.stereotype.Service;
 
 import java.util.List;
@@ -12,8 +11,7 @@
 public class CameoCommitService extends DefaultCommitService implements CommitService {
     @Override
     public boolean isProjectNew(String projectId) {
-        ContextHolder.setContext(projectId);
-        List<Commit> commits = commitRepository.findAll();
+        List<CommitJson> commits = commitPersistence.findAllByProjectId(projectId);
         return commits == null || commits.size() <= 1; // a cameo project gets 1 auto commit, so its still "new"
     }
 }

cameo/src/main/java/org/openmbee/mms/cameo/services/CameoHelper.java

@@ -6,12 +6,14 @@
 import java.util.Set;
 import org.openmbee.mms.cameo.CameoConstants;
 import org.openmbee.mms.cameo.CameoNodeType;
+import org.openmbee.mms.core.utils.ElementUtils;
 import org.openmbee.mms.json.ElementJson;
 import org.springframework.stereotype.Component;
 
 @Component
-public class CameoHelper {
+public class CameoHelper implements ElementUtils {
 
+    @Override
     public CameoNodeType getNodeType(ElementJson e) {
         if (isDocument(e)) {
             return CameoNodeType.DOCUMENT;