Merge branch 'release/2020-09'

app/Module.java

@@ -1,14 +1,29 @@
+/*
+ * SysML v2 REST/HTTP Pilot Implementation
+ * Copyright (C) 2020  InterCAX LLC
+ * Copyright (C) 2020  California Institute of Technology ("Caltech")
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ *
+ * @license LGPL-3.0-or-later <http://spdx.org/licenses/LGPL-3.0-or-later>
+ */
+
 import com.google.inject.AbstractModule;
 import config.MetamodelProvider;
 import config.impl.JPAMetamodelProvider;
-import dao.CommitDao;
-import dao.ElementDao;
-import dao.ProjectDao;
-import dao.RelationshipDao;
-import dao.impl.jpa.JpaCommitDao;
-import dao.impl.jpa.JpaElementDao;
-import dao.impl.jpa.JpaProjectDao;
-import dao.impl.jpa.JpaRelationshipDao;
+import dao.*;
+import dao.impl.jpa.*;
 import jackson.databind.ObjectMapperFactory;
 import jackson.databind.impl.HibernateObjectMapperFactory;
 import jpa.manager.JPAManager;
@@ -25,5 +40,6 @@ protected void configure() {
         bind(ProjectDao.class).to(JpaProjectDao.class);
         bind(RelationshipDao.class).to(JpaRelationshipDao.class);
         bind(CommitDao.class).to(JpaCommitDao.class);
+        bind(QueryDao.class).to(JpaQueryDao.class);
     }
 }

app/config/MetamodelProvider.java

@@ -1,3 +1,24 @@
+/*
+ * SysML v2 REST/HTTP Pilot Implementation
+ * Copyright (C) 2020  InterCAX LLC
+ * Copyright (C) 2020  California Institute of Technology ("Caltech")
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ *
+ * @license LGPL-3.0-or-later <http://spdx.org/licenses/LGPL-3.0-or-later>
+ */
+
 package config;
 
 import java.util.Set;

app/config/impl/JPAMetamodelProvider.java

@@ -1,25 +1,55 @@
+/*
+ * SysML v2 REST/HTTP Pilot Implementation
+ * Copyright (C) 2020  InterCAX LLC
+ * Copyright (C) 2020  California Institute of Technology ("Caltech")
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ *
+ * @license LGPL-3.0-or-later <http://spdx.org/licenses/LGPL-3.0-or-later>
+ */
+
 package config.impl;
 
 import config.MetamodelProvider;
 import org.omg.sysml.metamodel.MofObject;
-import org.omg.sysml.metamodel.impl.MofObjectImpl;
+import org.omg.sysml.query.Constraint;
+import org.omg.sysml.record.Record;
 import org.reflections.Reflections;
 
+import java.util.Arrays;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
 public class JPAMetamodelProvider implements MetamodelProvider {
-    private static Set<Class<?>> INTERFACES = new HashSet<>(), IMPLEMENTATION_CLASSES = new HashSet<>();
+    private static final Set<Class<?>> INTERFACES = new HashSet<>();
+    private static final Set<Class<?>> IMPLEMENTATION_CLASSES = new HashSet<>();
 
     static {
-        INTERFACES.add(MofObject.class);
-        for (String pakkage : new String[]{"org.omg.sysml.metamodel", "org.omg.sysml.extension", "org.omg.sysml.versioning"}) {
-            INTERFACES.addAll(new Reflections(pakkage).getSubTypesOf(MofObject.class));
-        }
-        IMPLEMENTATION_CLASSES.add(MofObjectImpl.class);
-        for (String pakkage : new String[]{"org.omg.sysml.metamodel.impl", "org.omg.sysml.extension.impl", "org.omg.sysml.versioning.impl"}) {
-            IMPLEMENTATION_CLASSES.addAll(new Reflections(pakkage).getSubTypesOf(MofObjectImpl.class));
-        }
+        List<Class<?>> roots = Arrays.asList(
+                MofObject.class,
+                Record.class,
+                Constraint.class
+        );
+        String packageScope = "org.omg.sysml";
+
+        INTERFACES.addAll(roots);
+        Reflections reflections = new Reflections(packageScope);
+        roots.stream()
+                .map(reflections::getSubTypesOf)
+                .flatMap(Set::stream)
+                .forEach(c -> (c.isInterface() ? INTERFACES : IMPLEMENTATION_CLASSES).add(c));
     }
 
     @Override

app/controllers/CommitController.java

@@ -1,6 +1,28 @@
+/*
+ * SysML v2 REST/HTTP Pilot Implementation
+ * Copyright (C) 2020  InterCAX LLC
+ * Copyright (C) 2020  California Institute of Technology ("Caltech")
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ *
+ * @license LGPL-3.0-or-later <http://spdx.org/licenses/LGPL-3.0-or-later>
+ */
+
 package controllers;
 
 import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import config.MetamodelProvider;
 import jackson.JacksonHelper;
 import org.omg.sysml.lifecycle.Commit;
@@ -19,11 +41,15 @@
 import java.util.UUID;
 
 public class CommitController extends Controller {
-    @Inject
-    private MetamodelProvider metamodelProvider;
+
+    private final MetamodelProvider metamodelProvider;
+    private final CommitService commitService;
 
     @Inject
-    private CommitService commitService;
+    public CommitController(CommitService commitService, MetamodelProvider metamodelProvider) {
+        this.commitService = commitService;
+        this.metamodelProvider = metamodelProvider;
+    }
 
     public Result byId(String id) {
         UUID uuid = UUID.fromString(id);
@@ -33,7 +59,7 @@ public Result byId(String id) {
 
     public Result all() {
         List<Commit> commits = commitService.getAll();
-        return ok(JacksonHelper.collectionValueToTree(List.class, metamodelProvider.getImplementationClass(Commit.class), commits));
+        return ok(JacksonHelper.collectionToTree(commits, List.class, metamodelProvider.getImplementationClass(Commit.class)));
     }
 
     public Result create(Http.Request request) {
@@ -54,13 +80,13 @@ public Result createWithProjectId(UUID projectId, Http.Request request) {
             return Results.badRequest();
         }
         requestedObject.setTimestamp(ZonedDateTime.now());
-        Optional<Commit> responseCommit = commitService.create(projectId, requestedObject);
-        return responseCommit.map(e -> created(Json.toJson(e))).orElseGet(Results::internalServerError);
+        Optional<Commit> response = commitService.create(projectId, requestedObject);
+        return response.map(e -> created(Json.toJson(e))).orElseGet(Results::internalServerError);
     }
 
     public Result byProject(UUID projectId) {
         List<Commit> commits = commitService.getByProjectId(projectId);
-        return ok(JacksonHelper.collectionValueToTree(List.class, metamodelProvider.getImplementationClass(Commit.class), commits, writer -> writer.withView(CommitImpl.Views.Compact.class)));
+        return ok(JacksonHelper.collectionToTree(commits, List.class, metamodelProvider.getImplementationClass(Commit.class), Json::mapper, writer -> writer.withView(CommitImpl.Views.Compact.class)));
     }
 
     public Result byProjectAndId(UUID projectId, UUID commitId) {
@@ -70,6 +96,6 @@ public Result byProjectAndId(UUID projectId, UUID commitId) {
 
     public Result headByProject(UUID projectId) {
         Optional<Commit> commit = commitService.getHeadByProjectId(projectId);
-        return commit.map(e -> ok(JacksonHelper.valueToTree(commit, writer -> writer.withView(CommitImpl.Views.Compact.class)))).orElseGet(Results::notFound);
+        return commit.map(e -> ok(JacksonHelper.objectToTree(commit, Json::mapper, mapper -> mapper.writer().withView(CommitImpl.Views.Compact.class), ObjectMapper::reader))).orElseGet(Results::notFound);
     }
 }

app/controllers/ElementController.java

@@ -1,3 +1,24 @@
+/*
+ * SysML v2 REST/HTTP Pilot Implementation
+ * Copyright (C) 2020  InterCAX LLC
+ * Copyright (C) 2020  California Institute of Technology ("Caltech")
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ *
+ * @license LGPL-3.0-or-later <http://spdx.org/licenses/LGPL-3.0-or-later>
+ */
+
 package controllers;
 
 import com.fasterxml.jackson.databind.JsonNode;
@@ -23,20 +44,18 @@
 
 import static jackson.JsonLdMofObjectAdornment.JSONLD_MIME_TYPE;
 
-/**
- * @author Manas Bajaj
- * <p>
- * Controller for handling all API requests related to SysML v2 elements
- */
 public class ElementController extends Controller {
-    @Inject
-    private MetamodelProvider metamodelProvider;
 
-    @Inject
-    private ElementService elementService;
+    private final ElementService elementService;
+    private final MetamodelProvider metamodelProvider;
+    private final Environment environment;
 
     @Inject
-    private Environment environment;
+    public ElementController(ElementService elementService, MetamodelProvider metamodelProvider, Environment environment) {
+        this.elementService = elementService;
+        this.metamodelProvider = metamodelProvider;
+        this.environment = environment;
+    }
 
     private static final boolean INLINE_JSON_LD_CONTEXT_DEFAULT = true;
     private static final boolean INLINE_JSON_LD_CONTEXT = Optional.ofNullable(System.getenv("INLINE_JSON_LD_CONTEXT"))
@@ -50,7 +69,7 @@ public Result byId(String id) {
 
     public Result all() {
         List<Element> elements = elementService.getAll();
-        return ok(JacksonHelper.collectionValueToTree(List.class, metamodelProvider.getImplementationClass(Element.class), elements));
+        return ok(JacksonHelper.collectionToTree(elements, List.class, metamodelProvider.getImplementationClass(Element.class)));
     }
 
     public Result create(Http.Request request) {
@@ -74,9 +93,9 @@ public Result getElementsByProjectIdCommitId(UUID projectId, UUID commitId, Http
                         )
                         .collect(Collectors.toSet())
         )
-                .map(set -> JacksonHelper.collectionValueToTree(Set.class, respondWithJsonLd ?
+                .map(set -> JacksonHelper.collectionToTree(set, Set.class, respondWithJsonLd ?
                         JsonLdMofObjectAdornment.class :
-                        metamodelProvider.getImplementationClass(Element.class), set)
+                        metamodelProvider.getImplementationClass(Element.class))
                 )
                 .map(Results::ok)
                 .map(result -> respondWithJsonLd ? result.as(JSONLD_MIME_TYPE) : result)
@@ -106,11 +125,10 @@ static JsonLdMofObjectAdornment adornMofObject(MofObject mof, Http.Request reque
     public Result getRootsByProjectIdCommitId(UUID projectId, UUID commitId, Http.Request request) {
         Set<Element> roots = elementService.getRootsByProjectIdCommitId(projectId, commitId);
         boolean respondWithJsonLd = respondWithJsonLd(request);
-        return ok(JacksonHelper.collectionValueToTree(Set.class,
-                respondWithJsonLd ? JsonLdMofObjectAdornment.class : metamodelProvider.getImplementationClass(Element.class),
-                roots.stream()
+        return ok(JacksonHelper.collectionToTree(roots.stream()
                         .map(e -> respondWithJsonLd ? adornMofObject(e, request, metamodelProvider, environment, projectId, commitId) : e)
-                        .collect(Collectors.toSet())
+                        .collect(Collectors.toSet()), Set.class,
+                respondWithJsonLd ? JsonLdMofObjectAdornment.class : metamodelProvider.getImplementationClass(Element.class)
         ));
     }
 

app/controllers/HomeController.java

@@ -1,3 +1,24 @@
+/*
+ * SysML v2 REST/HTTP Pilot Implementation
+ * Copyright (C) 2020  InterCAX LLC
+ * Copyright (C) 2020  California Institute of Technology ("Caltech")
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ *
+ * @license LGPL-3.0-or-later <http://spdx.org/licenses/LGPL-3.0-or-later>
+ */
+
 package controllers;
 
 import play.mvc.*;