RepositoryFile with ACL

- Upgrade path
- Using Path instead of `String path, String filename`
- FTP with RepositoryFolder
- RepositoryFolder with ACL support
- Unit tests updated
- Self-cleaning

file-repository-core/pom.xml

@@ -172,12 +172,6 @@
 			<artifactId>application-blocks-security</artifactId>
 			<version>1.5-SNAPSHOT</version>
 		</dependency>
-		<dependency>
-			<groupId>com.querydsl</groupId>
-			<artifactId>querydsl-jpa</artifactId>
-			<version>${querydsl.version}</version>
-			<scope>provided</scope>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.tika</groupId>
 			<artifactId>tika-core</artifactId>

file-repository-core/src/main/java/org/genesys/filerepository/FolderNotEmptyException.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.genesys.filerepository;
+
+/**
+ * The InvalidRepositoryPathException is thrown when Repository is not happy
+ * with your selected path.
+ */
+public class FolderNotEmptyException extends FileRepositoryException {
+	/** The Constant serialVersionUID. */
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * Instantiates a new invalid repository path exception.
+	 *
+	 * @param message the message
+	 */
+	public FolderNotEmptyException(final String message) {
+		super(message);
+	}
+}

file-repository-core/src/main/java/org/genesys/filerepository/migration/RepositoryUpgrade20180920.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.genesys.filerepository.migration;
+
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.List;
+
+import org.genesys.filerepository.model.QRepositoryFile;
+import org.genesys.filerepository.model.RepositoryFile;
+import org.genesys.filerepository.model.RepositoryFolder;
+import org.genesys.filerepository.persistence.RepositoryFilePersistence;
+import org.genesys.filerepository.service.RepositoryService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import com.querydsl.jpa.impl.JPAQueryFactory;
+
+/**
+ * Creates {@link RepositoryFolder} entries and their parents - Links all
+ * {@link RepositoryFile} to their parent folders
+ *
+ * @author Matija Obreza
+ */
+@Component
+public class RepositoryUpgrade20180920 {
+	private static final Logger LOG = LoggerFactory.getLogger(RepositoryUpgrade20180920.class);
+
+	/** The tx manager. */
+	@Autowired
+	@Qualifier("transactionManager")
+	protected PlatformTransactionManager txManager;
+
+	@Autowired
+	private RepositoryFilePersistence fileRepository;
+
+	@Autowired
+	private RepositoryService repositoryService;
+
+	@Autowired
+	private JPAQueryFactory jpaQueryFactory;
+
+	public void doUpgrade() throws Exception {
+		TransactionTemplate tmpl = new TransactionTemplate(txManager);
+		tmpl.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus status) {
+				try {
+					makeFolders();
+				} catch (Throwable e) {
+					LOG.error("Could not migrate 1.0 to 1.1 model: {}", e.getMessage(), e);
+				}
+			}
+		});
+
+		tmpl.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus status) {
+				try {
+					moveFilesToFolders();
+				} catch (Throwable e) {
+					LOG.error("Could not migrate 1.0 to 1.1 model: {}", e.getMessage(), e);
+				}
+			}
+		});
+	}
+
+	/**
+	 * Do the migration.
+	 *
+	 * @throws Exception the exception
+	 */
+	void makeFolders() throws Exception {
+		long count = 0;
+
+		// get distinct paths
+		List<String> paths = jpaQueryFactory.selectFrom(QRepositoryFile.repositoryFile).select(QRepositoryFile.repositoryFile.path).distinct().orderBy(
+			QRepositoryFile.repositoryFile.path.asc()).fetch();
+
+		for (String folderName : paths) {
+			final Path folderPath = Paths.get(folderName);
+			RepositoryFolder folder = repositoryService.getFolder(folderPath);
+
+			if (folder == null) {
+				LOG.warn("Creating repository path={}", folderPath);
+				folder = repositoryService.ensureFolder(folderPath);
+				LOG.warn("Created folder={}", folder.getFolderPath());
+				count++;
+			}
+		}
+
+		if (count == 0) {
+			LOG.warn("\n\n\t** All repository folders have been created **\n\t   You can remove the {} bean.\n\n", this.getClass().getName());
+		}
+	}
+
+	/**
+	 * Do the migration.
+	 *
+	 * @throws Exception the exception
+	 */
+	void moveFilesToFolders() throws Exception {
+		long count = 0;
+
+		for (RepositoryFile repoFile : fileRepository.findAll()) {
+			if (repoFile.getFolder() == null) {
+				RepositoryFolder repoFolder = repositoryService.getFolder(Paths.get(repoFile.getPath()));
+				if (repoFile.getFolder() == null || repoFile.getFolder().getId() != repoFolder.getId()) {
+					LOG.warn("Upgrading {} to folder={}", repoFile.getPath(), repoFolder.getPath());
+					repoFile.setFolder(repoFolder);
+					fileRepository.save(repoFile);
+					count++;
+				}
+			}
+		}
+
+		if (count == 0) {
+			LOG.warn("\n\n\t** All repository files have been moved to proper folders **\n\t   You can remove the {} bean.\n\n", this.getClass().getName());
+		}
+	}
+}

file-repository-core/src/main/java/org/genesys/filerepository/model/ImageGallery.java

@@ -16,6 +16,8 @@
 
 package org.genesys.filerepository.model;
 
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -28,6 +30,7 @@ import javax.persistence.Lob;
 import javax.persistence.ManyToMany;
 import javax.persistence.OrderColumn;
 import javax.persistence.Table;
+import javax.persistence.Transient;
 
 import org.genesys.blocks.model.AuditedVersionedModel;
 import org.genesys.blocks.model.Copyable;
@@ -78,6 +81,9 @@ public class ImageGallery extends AuditedVersionedModel implements AclAwareModel
 	@OrderColumn(name = "position")
 	private List<RepositoryImage> images;
 
+	@Transient
+	private Path folderPath;
+	
 	/**
 	 * Gets the path.
 	 *
@@ -175,4 +181,18 @@ public class ImageGallery extends AuditedVersionedModel implements AclAwareModel
 		copy.images = new ArrayList<>(this.images);
 		return copy;
 	}
+
+	/**
+	 * Gets the folder path.
+	 *
+	 * @return the folder path
+	 */
+	public Path getFolderPath() {
+		synchronized (this) {
+			if (folderPath == null) {
+				this.folderPath = Paths.get(this.path);
+			}
+		}
+		return this.folderPath;
+	}
 }

file-repository-core/src/main/java/org/genesys/filerepository/model/RepositoryDocument.java

@@ -20,6 +20,7 @@ import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.Lob;
 import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 
 import org.genesys.filerepository.metadata.DocumentMetadata;
@@ -53,6 +54,7 @@ public class RepositoryDocument extends RepositoryFile implements DocumentMetada
 	 */
 	@Override
 	@PrePersist
+	@PreUpdate
 	protected void prePersist() {
 		// Don't forget the superclass!
 		super.prePersist();

file-repository-core/src/main/java/org/genesys/filerepository/model/RepositoryFile.java

@@ -16,11 +16,14 @@
 
 package org.genesys.filerepository.model;
 
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Date;
 import java.util.UUID;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
@@ -28,33 +31,41 @@ import javax.persistence.Index;
 import javax.persistence.Inheritance;
 import javax.persistence.InheritanceType;
 import javax.persistence.Lob;
+import javax.persistence.ManyToOne;
 import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
-import javax.persistence.Transient;
 import javax.persistence.UniqueConstraint;
 
 import org.apache.commons.lang3.StringUtils;
 import org.genesys.blocks.model.AuditedVersionedModelWithoutId;
 import org.genesys.blocks.model.Copyable;
 import org.genesys.blocks.model.InMemoryIdGenerator;
+import org.genesys.blocks.model.SelfCleaning;
 import org.genesys.blocks.security.model.AclAwareModel;
 import org.genesys.filerepository.metadata.BaseMetadata;
 import org.genesys.filerepository.service.BytesStorageService;
 import org.hibernate.annotations.Type;
 
+import com.fasterxml.jackson.annotation.JsonIdentityInfo;
+import com.fasterxml.jackson.annotation.JsonIdentityReference;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonProperty.Access;
+import com.fasterxml.jackson.annotation.ObjectIdGenerators;
+
 /**
  * The RepositoryFile.
  */
 @Entity
 @Table(name = "repository_file",
 		// indexes
-		indexes = { @Index(unique = false, columnList = "path", name = "IX_repoFile_path") }
+		indexes = { @Index(unique = false, columnList = "folder_id", name = "IX_repoFile_path") }
 		// unique
-		, uniqueConstraints = { @UniqueConstraint(columnNames = { "path", "originalFilename" }) })
+		, uniqueConstraints = { @UniqueConstraint(columnNames = { "folder_id", "originalFilename" }) })
 @Inheritance(strategy = InheritanceType.TABLE_PER_CLASS)
-public class RepositoryFile extends AuditedVersionedModelWithoutId implements AclAwareModel, BaseMetadata, Copyable<RepositoryFile> {
+public class RepositoryFile extends AuditedVersionedModelWithoutId implements AclAwareModel, BaseMetadata, Copyable<RepositoryFile>, SelfCleaning {
 
 	/** The Constant serialVersionUID. */
 	private static final long serialVersionUID = -4816923593950502695L;
@@ -70,11 +81,21 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 	@Type(type = "uuid-binary")
 	private UUID uuid;
 
-	/** The path. */
-	// Path in the repository
-	@Column(nullable = false, length = 250)
+	/** Path in the repository. */
+	@Column(length = 250)
 	private String path;
 
+	/**
+	 * The repository folder.
+	 *
+	 * @since 1.1
+	 */
+	@ManyToOne(cascade = {}, fetch = FetchType.LAZY, optional = false)
+	@JsonIdentityInfo(generator = ObjectIdGenerators.PropertyGenerator.class, property = "path")
+	@JsonIdentityReference(alwaysAsId = true)
+	@JsonProperty(access = Access.READ_ONLY)
+	private RepositoryFolder folder;
+
 	/** The original filename as provided by the end user. */
 	@Column(nullable = false, length = 250)
 	private String originalFilename;
@@ -90,7 +111,7 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 	/** The subject. */
 	@Column
 	@Lob
-	@Type(type = "org.hibernate.type.TextType")	
+	@Type(type = "org.hibernate.type.TextType")
 	private String subject;
 
 	/** The description. */
@@ -158,13 +179,25 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 	private int size;
 
 	/**
-	 * Pre persist.
+	 * Before persist and any update
 	 */
 	@PrePersist
+	@PreUpdate
 	protected void prePersist() {
 		if (uuid == null) {
 			uuid = UUID.randomUUID();
 		}
+		
+		trimStringsToNull();
+	}
+
+	/**
+	 * For repository files, the parent object is always a {@link RepositoryFolder}
+	 * (can't be null).
+	 */
+	@Override
+	public AclAwareModel aclParentObject() {
+		return this.folder;
 	}
 
 	/*
@@ -184,7 +217,7 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 	 * @return relative URL to the file resource
 	 */
 	public String getUrl() {
-		return getStorageFullPath();
+		return getStorageFullPath().toString();
 	}
 
 	/**
@@ -225,11 +258,11 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 	 *
 	 * @return the storage path
 	 */
-	public String getStoragePath() {
+	public Path getStoragePath() {
 		if (uuid == null) {
 			return null;
 		}
-		return "/" + uuid.toString().substring(0, 3);
+		return Paths.get("/", uuid.toString().substring(0, 3));
 	}
 
 	/**
@@ -238,8 +271,8 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 	 *
 	 * @return the storage full path
 	 */
-	public String getStorageFullPath() {
-		return getStoragePath() + "/" + getFilename();
+	public Path getStorageFullPath() {
+		return getStoragePath().resolve(getFilename());
 	}
 
 	/*
@@ -544,24 +577,6 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 		this.extension = extension;
 	}
 
-	/**
-	 * Gets the path.
-	 *
-	 * @return the path
-	 */
-	public String getPath() {
-		return path;
-	}
-
-	/**
-	 * Sets the path.
-	 *
-	 * @param path the new path
-	 */
-	public void setPath(final String path) {
-		this.path = path;
-	}
-
 	/**
 	 * Gets the original url.
 	 *
@@ -652,19 +667,55 @@ public class RepositoryFile extends AuditedVersionedModelWithoutId implements Ac
 		this.size = size;
 	}
 
+	/**
+	 * Gets the folder.
+	 *
+	 * @return the folder
+	 */
+	public RepositoryFolder getFolder() {
+		return folder;
+	}
+
+	/**
+	 * Sets the folder.
+	 *
+	 * @param folder the new folder
+	 */
+	public void setFolder(RepositoryFolder folder) {
+		this.folder = folder;
+	}
+
+	/**
+	 * Gets the path.
+	 *
+	 * @return the path
+	 */
+	public String getPath() {
+		return path;
+	}
+
+	/**
+	 * Sets the path.
+	 *
+	 * @param path the new path
+	 */
+	public void setPath(String path) {
+		this.path = path;
+	}
+
 	/*
 	 * (non-Javadoc)
 	 * @see org.genesys.blocks.model.Copyable#apply(java.lang.Object)
 	 */
 	@Override
 	public RepositoryFile apply(final RepositoryFile source) {
-		this.path = StringUtils.defaultIfBlank(source.path, this.path);
 		if (StringUtils.isNotBlank(source.originalFilename)) {
 			// also updates extension
 			setOriginalFilename(source.originalFilename);
 		}
 
 		this.active = source.active;
+		this.folder = source.folder;
 		this.accessRights = source.accessRights;
 		this.bibliographicCitation = source.bibliographicCitation;
 		this.contentType = source.contentType;

file-repository-core/src/main/java/org/genesys/filerepository/model/RepositoryFolder.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.genesys.filerepository.model;
+
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.List;
+import java.util.UUID;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.Lob;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.PrePersist;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.genesys.blocks.model.UuidModel;
+import org.genesys.blocks.security.model.AclAwareModel;
+import org.genesys.filerepository.InvalidRepositoryPathException;
+import org.genesys.filerepository.service.impl.PathValidator;
+import org.hibernate.annotations.Type;
+
+import com.fasterxml.jackson.annotation.JsonIdentityInfo;
+import com.fasterxml.jackson.annotation.JsonIdentityReference;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.ObjectIdGenerators;
+
+/**
+ * <b>Repository Folder</b> represents a location (path) of files in the
+ * repository. It is immutable and it's <code>path</code> cannot be modified.
+ * 
+ * @since 1.1-SNAPSHOT
+ */
+@Entity
+@Table(name = "repositoryfolder")
+public class RepositoryFolder extends UuidModel implements AclAwareModel {
+
+	/** The Constant serialVersionUID. */
+	private static final long serialVersionUID = -7947000802758739238L;
+
+	/**
+	 * Reference to parent Folder. Root folders have this set to null. This
+	 * establishes hierarchical structure of folders.
+	 * 
+	 * Because paths are immutable, this cannot be updated.
+	 */
+	@ManyToOne(cascade = {}, optional = true, fetch = FetchType.LAZY)
+	@JoinColumn(updatable = false)
+	@JsonIgnore
+	private RepositoryFolder parent;
+
+	/**
+	 * List of sub-folders.
+	 */
+	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "parent")
+	@JsonIdentityInfo(generator = ObjectIdGenerators.PropertyGenerator.class, property = "path")
+	@JsonIdentityReference(alwaysAsId = true)
+	private List<RepositoryFolder> children;
+
+	/** List of files in this folder. */
+	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "folder")
+	// @JsonIdentityInfo(generator = ObjectIdGenerators.PropertyGenerator.class,
+	// property = "originalFilename")
+	// @JsonIdentityReference(alwaysAsId = true)
+	@JsonIgnore
+	private List<RepositoryFile> files;
+
+	/**
+	 * The name of the folder within parent Folder. It is immutable and must not be
+	 * updated.
+	 */
+	@Column(name = "name", nullable = false, updatable = false)
+	private String name;
+
+	/**
+	 * Unique path in the repository. It is immutable and must not be updated. It is
+	 * based on the parent Folder path + name.
+	 */
+	@Column(name = "path", nullable = false, unique = true, updatable = false)
+	private String path;
+
+	/**
+	 * A human-friendly folder title, not to be confused with {@link #name} above.
+	 */
+	@Column
+	private String title;
+
+	/** Folder description. */
+	@Lob
+	@Type(type = "org.hibernate.type.TextType")
+	private String description;
+
+	/** The folder path. */
+	@Transient
+	private Path folderPath;
+
+	/**
+	 * Pre persist.
+	 */
+	@PrePersist
+	protected void prePersist() {
+		if (uuid == null) {
+			uuid = UUID.randomUUID();
+		}
+		this.path = this.parent == null ? "/" + this.name : this.parent.getFolderPath().resolve(this.name).normalize().toAbsolutePath().toString();
+	}
+
+	/**
+	 * The parent folder is generally the parent object for any folder.
+	 *
+	 * @return the ACL parent object
+	 */
+	@Override
+	public AclAwareModel aclParentObject() {
+		return this.parent;
+	}
+
+	/**
+	 * Gets the parent.
+	 *
+	 * @return the parent
+	 */
+	public RepositoryFolder getParent() {
+		return parent;
+	}
+
+	/**
+	 * Sets the parent.
+	 *
+	 * @param parent the new parent
+	 */
+	public void setParent(RepositoryFolder parent) {
+		this.parent = parent;
+	}
+
+	/**
+	 * Gets the children.
+	 *
+	 * @return the children
+	 */
+	public List<RepositoryFolder> getChildren() {
+		return children;
+	}
+
+	/**
+	 * Sets the children.
+	 *