Create new project from project backup

pom.xml

@@ -96,7 +96,7 @@
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-ipc</artifactId>
-            <version>1.0.9</version>
+            <version>1.0.10</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>

src/main/java/edu/stanford/protege/webprotege/ApplicationBeansConfiguration.java

@@ -19,6 +19,7 @@
 import edu.stanford.protege.webprotege.hierarchy.NamedHierarchyManager;
 import edu.stanford.protege.webprotege.hierarchy.NamedHierarchyManagerImpl;
 import edu.stanford.protege.webprotege.hierarchy.NamedHierarchyRepository;
+import edu.stanford.protege.webprotege.icd.projects.*;
 import edu.stanford.protege.webprotege.index.*;
 import edu.stanford.protege.webprotege.inject.*;
 import edu.stanford.protege.webprotege.inject.project.ProjectDirectoryFactory;
@@ -189,12 +190,8 @@ OWLDataFactory getOwlDataFactory() {
     }
 
     @Bean
-    ProjectDirectoryFactory getProjectDirectoryFactory() {
-        return new ProjectDirectoryFactory(getDataDirectory());
-    }
-
-    private File getDataDirectory() {
-        return null;
+    ProjectDirectoryFactory getProjectDirectoryFactory(DataDirectoryProvider dataDirectoryProvider) {
+        return new ProjectDirectoryFactory(dataDirectoryProvider.get());
     }
 
     @Bean
@@ -575,6 +572,11 @@ CommandExecutor<CreateInitialRevisionHistoryRequest, CreateInitialRevisionHistor
         return new CommandExecutorImpl<>(CreateInitialRevisionHistoryResponse.class);
     }
 
+    @Bean
+    CommandExecutor<PrepareBackupFilesForUseRequest, PrepareBackupFilesForUseResponse> executorForPrepareBackupFilesForUse() {
+        return new CommandExecutorImpl<>(PrepareBackupFilesForUseResponse.class);
+    }
+
     @Bean
     MinioClient minioClient(MinioProperties properties) {
         return MinioClient.builder()

src/main/java/edu/stanford/protege/webprotege/ProjectActionHandlerBeansConfiguration.java

@@ -23,6 +23,8 @@
 import edu.stanford.protege.webprotege.icd.hierarchy.ClassHierarchyRetiredClassDetector;
 import edu.stanford.protege.webprotege.index.*;
 import edu.stanford.protege.webprotege.individuals.*;
+import edu.stanford.protege.webprotege.inject.ProjectBackupDirectoryProvider;
+import edu.stanford.protege.webprotege.inject.project.ProjectDirectoryProvider;
 import edu.stanford.protege.webprotege.ipc.EventDispatcher;
 import edu.stanford.protege.webprotege.issues.*;
 import edu.stanford.protege.webprotege.lang.*;
@@ -741,6 +743,18 @@ GetProjectInfoActionHandler getProjectInfoActionHandler(AccessManager p1,
         return new GetProjectInfoActionHandler(p1, p2, p3);
     }
 
+    @Bean
+    public ProjectBackupManager getProjectBackupManager(ProjectDirectoryProvider p1,
+                                                        ProjectBackupDirectoryProvider p2) {
+        return new ProjectBackupManager(p1, p2);
+    }
+
+    @Bean
+    CreateBackupOwlFileActionHandler createBackupOwlFileActionHandler(AccessManager p1,
+                                                                      ProjectBackupManager p2) {
+        return new CreateBackupOwlFileActionHandler(p1, p2);
+    }
+
 
     @Bean
     GetHierarchySiblingsActionHandler getHierarchySiblingsActionHandler(AccessManager p1,

src/main/java/edu/stanford/protege/webprotege/ProjectBeansConfiguration.java

@@ -1166,14 +1166,18 @@ ClassFrameProviderImpl classFrameProvider(Class2ClassFrameTranslatorFactory p1)
         return new ClassFrameProviderImpl(p1);
     }
 
+    @Bean
+    ProjectBackupDirectoryProvider projectBackupDirectoryProvider(ProjectId projectId){
+        return new ProjectBackupDirectoryProvider(projectId);
+    }
+
     @Bean
     @LuceneIndexesDirectory
     Path luceneIndexesDirectory(DataDirectoryProvider dataDirectoryProvider) {
         var dataDirectory = dataDirectoryProvider.get().toPath();
         return dataDirectory.resolve("lucene-indexes");
 
     }
-
     @Bean
     ActiveLanguagesManagerImpl activeLanguagesManager(ProjectId p1,
                                                       AxiomsByEntityReferenceIndex p2,

src/main/java/edu/stanford/protege/webprotege/change/AbstractCreateEntitiesChangeListGenerator.java

@@ -142,7 +142,7 @@ public OntologyChangeList<Set<E>> generateChanges(ChangeGenerationContext contex
                 OWLAnnotationProperty titleProperty = dataFactory.getOWLAnnotationProperty(propertyIRITitle);
 
                 OWLLiteral literal = dataFactory.getOWLLiteral(sourceText, langTag);
-                OWLNamedIndividual titleIndividual = dataFactory.getOWLNamedIndividual(IRI.create(IcdConstants.NS, "TitleTerm_"+sourceText.replace(" ","_")));
+                OWLNamedIndividual titleIndividual = dataFactory.getOWLNamedIndividual(IRI.create(IcdConstants.NS, "TitleTerm_"+UUID.randomUUID()));
 
                 OWLAnnotationAssertionAxiom titleAxiom = dataFactory.getOWLAnnotationAssertionAxiom(titleProperty, freshEntity.getIRI(), titleIndividual.getIRI());
                 OWLAnnotationAssertionAxiom newLabelAxiom = dataFactory.getOWLAnnotationAssertionAxiom(labelProperty, titleIndividual.getIRI(), literal);

src/main/java/edu/stanford/protege/webprotege/icd/exceptions/FileActionException.java

@@ -0,0 +1,7 @@
+package edu.stanford.protege.webprotege.icd.exceptions;
+
+public class FileActionException extends RuntimeException {
+    public FileActionException(String message, Throwable exception) {
+        super(message, exception);
+    }
+}

src/main/java/edu/stanford/protege/webprotege/icd/projects/PrepareBackupFilesForUseRequest.java

@@ -0,0 +1,21 @@
+package edu.stanford.protege.webprotege.icd.projects;
+
+import com.fasterxml.jackson.annotation.*;
+import edu.stanford.protege.webprotege.common.*;
+import edu.stanford.protege.webprotege.csv.DocumentId;
+
+import static edu.stanford.protege.webprotege.icd.projects.PrepareBackupFilesForUseRequest.CHANNEL;
+
+@JsonTypeName(CHANNEL)
+public record PrepareBackupFilesForUseRequest(
+        @JsonProperty("projectId") ProjectId projectId,
+        @JsonProperty("fileSubmissionId") DocumentId fileSubmissionId
+) implements Request<PrepareBackupFilesForUseResponse> {
+
+    public static final String CHANNEL = "icatx.versioning.PrepareBinaryFileBackupForUse";
+
+    @Override
+    public String getChannel() {
+        return CHANNEL;
+    }
+}

src/main/java/edu/stanford/protege/webprotege/icd/projects/PrepareBackupFilesForUseResponse.java

@@ -0,0 +1,13 @@
+package edu.stanford.protege.webprotege.icd.projects;
+
+import com.fasterxml.jackson.annotation.*;
+import edu.stanford.protege.webprotege.common.BlobLocation;
+import edu.stanford.protege.webprotege.dispatch.Result;
+
+import static edu.stanford.protege.webprotege.icd.projects.PrepareBackupFilesForUseRequest.CHANNEL;
+
+@JsonTypeName(CHANNEL)
+public record PrepareBackupFilesForUseResponse(
+        @JsonProperty("binaryFileLocation") BlobLocation binaryFileLocation
+) implements Result {
+}

src/main/java/edu/stanford/protege/webprotege/inject/ProjectBackupDirectoryProvider.java

@@ -0,0 +1,26 @@
+package edu.stanford.protege.webprotege.inject;
+
+import edu.stanford.protege.webprotege.common.ProjectId;
+import org.springframework.beans.factory.annotation.Value;
+
+import javax.inject.Provider;
+import java.io.File;
+import java.nio.file.Path;
+
+public class ProjectBackupDirectoryProvider implements Provider<File> {
+
+    @Value("${webprotege.directories.backup}")
+    private Path backupDirectory;
+
+    private ProjectId projectId;
+
+    public ProjectBackupDirectoryProvider(ProjectId projectId) {
+        this.projectId = projectId;
+    }
+
+
+    @Override
+    public File get() {
+        return new File(backupDirectory.toFile(), projectId.id());
+    }
+}

src/main/java/edu/stanford/protege/webprotege/project/CreateBackupOwlFileAction.java

@@ -0,0 +1,26 @@
+package edu.stanford.protege.webprotege.project;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonTypeName;
+import edu.stanford.protege.webprotege.common.ProjectId;
+import edu.stanford.protege.webprotege.dispatch.ProjectAction;
+
+import javax.annotation.Nonnull;
+
+import static edu.stanford.protege.webprotege.project.CreateBackupOwlFileAction.CHANNEL;
+
+@JsonTypeName(CHANNEL)
+
+public record CreateBackupOwlFileAction(@JsonProperty("projectId") ProjectId projectId) implements ProjectAction<CreateBackupOwlFileResponse>, HasProjectId {
+    public final static String CHANNEL = "webprotege.projects.CreateBackupOwlFile";
+
+    @Override
+    public String getChannel() {
+        return CHANNEL;
+    }
+    @Nonnull
+    @Override
+    public ProjectId projectId() {
+        return projectId;
+    }
+}

src/main/java/edu/stanford/protege/webprotege/project/CreateBackupOwlFileActionHandler.java

@@ -0,0 +1,32 @@
+package edu.stanford.protege.webprotege.project;
+
+import edu.stanford.protege.webprotege.access.AccessManager;
+import edu.stanford.protege.webprotege.dispatch.AbstractProjectActionHandler;
+import edu.stanford.protege.webprotege.ipc.ExecutionContext;
+import org.jetbrains.annotations.NotNull;
+
+import java.nio.file.Path;
+
+public class CreateBackupOwlFileActionHandler extends AbstractProjectActionHandler<CreateBackupOwlFileAction, CreateBackupOwlFileResponse> {
+
+    private final ProjectBackupManager projectBackupManager;
+
+    public CreateBackupOwlFileActionHandler(@NotNull AccessManager accessManager, ProjectBackupManager projectBackupManager) {
+        super(accessManager);
+        this.projectBackupManager = projectBackupManager;
+    }
+
+    @NotNull
+    @Override
+    public Class<CreateBackupOwlFileAction> getActionClass() {
+        return CreateBackupOwlFileAction.class;
+    }
+
+
+    @NotNull
+    @Override
+    public CreateBackupOwlFileResponse execute(@NotNull CreateBackupOwlFileAction action, @NotNull ExecutionContext executionContext) {
+        Path owlBackupFile  = projectBackupManager.createBackup();
+        return new CreateBackupOwlFileResponse(owlBackupFile.toString());
+    }
+}

src/main/java/edu/stanford/protege/webprotege/project/CreateBackupOwlFileCommandHandler.java

@@ -0,0 +1,34 @@
+package edu.stanford.protege.webprotege.project;
+
+import edu.stanford.protege.webprotege.api.ActionExecutor;
+import edu.stanford.protege.webprotege.ipc.CommandHandler;
+import edu.stanford.protege.webprotege.ipc.ExecutionContext;
+import edu.stanford.protege.webprotege.ipc.WebProtegeHandler;
+import org.jetbrains.annotations.NotNull;
+import reactor.core.publisher.Mono;
+
+@WebProtegeHandler
+public class CreateBackupOwlFileCommandHandler implements CommandHandler<CreateBackupOwlFileAction, CreateBackupOwlFileResponse> {
+    private final ActionExecutor executor;
+
+    public CreateBackupOwlFileCommandHandler(ActionExecutor executor) {
+        this.executor = executor;
+    }
+
+    @NotNull
+    @Override
+    public String getChannelName() {
+        return CreateBackupOwlFileAction.CHANNEL;
+    }
+
+    @Override
+    public Class<CreateBackupOwlFileAction> getRequestClass() {
+        return CreateBackupOwlFileAction.class;
+    }
+
+    @Override
+    public Mono<CreateBackupOwlFileResponse> handleRequest(CreateBackupOwlFileAction request, ExecutionContext executionContext) {
+        var result = executor.execute(request, new ExecutionContext(executionContext.userId(), executionContext.jwt()));
+        return Mono.just(result);
+    }
+}

src/main/java/edu/stanford/protege/webprotege/project/CreateBackupOwlFileResponse.java

@@ -0,0 +1,11 @@
+package edu.stanford.protege.webprotege.project;
+
+import com.fasterxml.jackson.annotation.*;
+import edu.stanford.protege.webprotege.common.Response;
+import edu.stanford.protege.webprotege.dispatch.Result;
+
+import static edu.stanford.protege.webprotege.project.CreateBackupOwlFileAction.CHANNEL;
+
+@JsonTypeName(CHANNEL)
+public record CreateBackupOwlFileResponse(@JsonProperty("owlFileBackupLocation") String owlFileBackupLocation) implements Result, Response {
+}

src/main/java/edu/stanford/protege/webprotege/project/CreateNewProjectFromProjectBackupAction.java

@@ -0,0 +1,48 @@
+package edu.stanford.protege.webprotege.project;
+
+import com.fasterxml.jackson.annotation.*;
+import com.google.common.base.Objects;
+import edu.stanford.protege.webprotege.common.ProjectId;
+import edu.stanford.protege.webprotege.dispatch.Action;
+
+import static com.google.common.base.MoreObjects.toStringHelper;
+
+@JsonTypeName(CreateNewProjectFromProjectBackupAction.CHANNEL)
+public record CreateNewProjectFromProjectBackupAction(
+        @JsonProperty("newProjectId") ProjectId newProjectId,
+        @JsonProperty("newProjectSettings") NewProjectSettings newProjectSettings
+) implements Action<CreateNewProjectFromProjectBackupResult> {
+
+    public static final String CHANNEL = "webprotege.projects.CreateNewProjectFromProjectBackup";
+
+    @Override
+    public String getChannel() {
+        return CHANNEL;
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hashCode(newProjectId, newProjectSettings);
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == this) {
+            return true;
+        }
+        if (!(obj instanceof CreateNewProjectFromProjectBackupAction other)) {
+            return false;
+        }
+        return this.newProjectId.equals(other.newProjectId) && this.newProjectSettings.equals(other.newProjectSettings);
+    }
+
+    @Override
+    public String toString() {
+        return toStringHelper("CreateNewProjectFromProjectBackupAction")
+                .addValue(newProjectId)
+                .addValue(newProjectSettings)
+                .toString();
+    }
+
+
+}

src/main/java/edu/stanford/protege/webprotege/project/CreateNewProjectFromProjectBackupCommandHandler.java

@@ -0,0 +1,55 @@
+package edu.stanford.protege.webprotege.project;
+
+import edu.stanford.protege.webprotege.authorization.*;
+import edu.stanford.protege.webprotege.ipc.*;
+import reactor.core.publisher.Mono;
+
+import javax.annotation.Nonnull;
+import java.util.*;
+
+import static edu.stanford.protege.webprotege.access.BuiltInAction.*;
+
+
+@WebProtegeHandler
+public class CreateNewProjectFromProjectBackupCommandHandler implements AuthorizedCommandHandler<CreateNewProjectFromProjectBackupAction, CreateNewProjectFromProjectBackupResult> {
+
+
+    private final CreateProjectSagaManager createProjectSagaManager;
+
+
+    public CreateNewProjectFromProjectBackupCommandHandler(CreateProjectSagaManager createProjectSagaManager) {
+        this.createProjectSagaManager = createProjectSagaManager;
+    }
+
+    @Nonnull
+    @Override
+    public String getChannelName() {
+        return CreateNewProjectFromProjectBackupAction.CHANNEL;
+    }
+
+    @Override
+    public Class<CreateNewProjectFromProjectBackupAction> getRequestClass() {
+        return CreateNewProjectFromProjectBackupAction.class;
+    }
+
+    @Override
+    public Mono<CreateNewProjectFromProjectBackupResult> handleRequest(CreateNewProjectFromProjectBackupAction request,
+                                                                       ExecutionContext executionContext) {
+        var result = createProjectSagaManager.executeFromBackup(request.newProjectSettings(), executionContext);
+        return Mono.fromFuture(result);
+    }
+
+    @Nonnull
+    @Override
+    public Resource getTargetResource(CreateNewProjectFromProjectBackupAction request) {
+        return ApplicationResource.get();
+    }
+
+    @Nonnull
+    @Override
+    public Collection<ActionId> getRequiredCapabilities() {
+        return List.of(CREATE_EMPTY_PROJECT.getActionId(), UPLOAD_PROJECT.getActionId());
+    }
+
+
+}