diff --git a/.gitignore b/.gitignore
index c6fdfc4d387f8be1bb3a4f51a73230aabcc9b02b..a76a3a9fa4aa990310cced6e486b1934da9bb80b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,6 +15,7 @@
# typical build dirs
build/
bin/
+lib/
target/
_apidoc/
src/doc/development/api/xml/out/
diff --git a/src/main/java/org/caosdb/server/database/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
deleted file mode 100644
index ad8810418015deebc81a587f30ce904ac3401a4a..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ /dev/null
@@ -1,402 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero 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 Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database;
-
-import com.google.common.base.Objects;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Domain;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.filesystem.FileSystem.ObjectType;
-import org.caosdb.server.filesystem.Hash;
-import org.caosdb.server.filesystem.Path;
-
-public class DatabaseUtils {
-
- public static final String bytes2UTF8(final byte[] bytes) {
- if (bytes == null) {
- return null;
- } else {
- return new String(bytes);
- }
- }
-
- private static Domain makeReplacement(final EntityInterface p) {
- // add a new helper domain.
- final Domain d =
- new Domain(p.getProperties(), p.getDatatype(), p.getValue(), p.getStatementStatus());
- d.setDescOverride(p.isDescOverride());
- d.setNameOverride(p.isNameOverride());
- d.setDatatypeOverride(p.isDatatypeOverride());
- d.setName(p.getName());
- d.setDescription(p.getDescription());
- p.setReplacement(d);
- return d;
- }
-
- public static void deriveStage1Inserts(
- final List<EntityInterface> stage1Inserts, final EntityInterface e) {
- // entity value
- if (e.hasValue()) {
- final Property p = new Property(e);
- p.setStatementStatus(StatementStatus.FIX);
- p.setPIdx(0);
- processPropertiesStage1(stage1Inserts, p, e);
- }
-
- for (final EntityInterface p : e.getProperties()) {
- processPropertiesStage1(stage1Inserts, p, e);
- }
- }
-
- private static void processPropertiesStage1(
- final List<EntityInterface> stage1Inserts, final EntityInterface p, final EntityInterface e) {
- stage1Inserts.add(p);
- if (!p.isDescOverride()
- && !p.isNameOverride()
- && !p.isDatatypeOverride()
- && (!p.hasProperties() || hasUniquePropertyId(p, e))
- && !(p.getDatatype() instanceof AbstractCollectionDatatype)) {
- // if p has no sub-properties, just add it
- } else {
- stage1Inserts.add(makeReplacement(p));
- }
- processSubPropertiesStage1(stage1Inserts, p);
- }
-
- public static int deriveStage2Inserts(
- final List<EntityInterface> stage2Inserts, final List<EntityInterface> stage1Inserts) {
- int domainCount = 0;
- for (final EntityInterface p : stage1Inserts) {
- if (p.hasRole() && p.getRole() == Role.Domain) {
- domainCount++;
- }
- if (!p.hasReplacement() && p.hasProperties()) {
- stage2Inserts.addAll(p.getProperties());
- }
- }
- return domainCount;
- }
-
- private static boolean hasUniquePropertyId(final EntityInterface p, final EntityInterface e) {
- final EntityID id = p.getId();
- for (final EntityInterface p2 : e.getProperties()) {
- if (Objects.equal(p2.getId(), id) && p2 != p) {
- return false;
- }
- }
- return true;
- }
-
- private static void processSubPropertiesStage1(
- final List<EntityInterface> stage1Inserts, final EntityInterface p) {
- for (final EntityInterface subP : p.getProperties()) {
- if (subP.hasProperties()) {
- stage1Inserts.add(makeReplacement(subP));
- processSubPropertiesStage1(stage1Inserts, subP);
- }
- }
- }
-
- public static void parseFromSparseEntities(final EntityInterface e, final SparseEntity spe) {
- if (spe != null) {
- e.parseSparseEntity(spe);
- }
- }
-
- public static void parseOverrides(final List<FlatProperty> properties, final ResultSet rs)
- throws SQLException {
- while (rs.next()) {
- final int property_id = rs.getInt("property_id");
- for (final FlatProperty p : properties) {
- if (p.id == property_id) {
- final String name = bytes2UTF8(rs.getBytes("name_override"));
- if (name != null) {
- p.name = name;
- }
- final String desc = bytes2UTF8(rs.getBytes("desc_override"));
- if (desc != null) {
- p.desc = desc;
- }
- final String type = bytes2UTF8(rs.getBytes("type_override"));
- if (type != null) {
- p.type = type;
- }
- final String coll = bytes2UTF8(rs.getBytes("collection_override"));
- if (coll != null) {
- p.collection = coll;
- }
- }
- }
- }
- }
-
- public static List<FlatProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
- final ArrayList<FlatProperty> ret = new ArrayList<FlatProperty>();
- while (rs.next()) {
- final FlatProperty fp = new FlatProperty();
- fp.id = rs.getInt("PropertyID");
- fp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
- fp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
- fp.idx = rs.getInt("PropertyIndex");
- ret.add(fp);
- }
- return ret;
- }
-
- /**
- * Helper function for parsing MySQL results.
- *
- * <p>This function creates SparseEntities and parses only the name, the role and the acl of an
- * entity.
- *
- * <p>Never returns null.
- */
- public static SparseEntity parseNameRoleACL(final ResultSet rs) throws SQLException {
- final SparseEntity ret = new SparseEntity();
- ret.role = bytes2UTF8(rs.getBytes("EntityRole"));
- ret.name = bytes2UTF8(rs.getBytes("EntityName"));
- ret.acl = bytes2UTF8(rs.getBytes("ACL"));
- return ret;
- }
-
- /**
- * Helper function for parsing MySQL results.
- *
- * <p>This function creates SparseEntities and parses all fields which belong to a SparseEntity:
- * id, name, role, acl, description, datatype, and the file properties.
- *
- * <p>Never returns null.
- */
- public static SparseEntity parseEntityResultSet(final ResultSet rs) throws SQLException {
- final SparseEntity ret = parseNameRoleACL(rs);
- ret.id = rs.getInt("EntityID");
- ret.description = bytes2UTF8(rs.getBytes("EntityDesc"));
- ret.datatype = bytes2UTF8(rs.getBytes("Datatype"));
- ret.collection = bytes2UTF8(rs.getBytes("Collection"));
- ret.versionId = bytes2UTF8(rs.getBytes("Version"));
-
- parseFSODescriptorFields(rs, ret);
- return ret;
- }
-
- public static void parseFSODescriptorFields(final ResultSet rs, final SparseEntity ret)
- throws SQLException {
- final String key = bytes2UTF8(rs.getBytes("FileKey"));
- if (key != null) {
- // ret.fileParentId = rs.getInt("FileParentID");
- ret.filePath = new Path(bytes2UTF8(rs.getBytes("FilePath")));
- ret.fileSize = rs.getLong("FileSize");
- if (rs.wasNull()) {
- ret.fileSize = null;
- }
- ret.fileHash =
- Hash.create(
- bytes2UTF8(rs.getBytes("FileHash")),
- rs.getLong("FileHashChecked"),
- bytes2UTF8(rs.getBytes("FileHashAlgo")));
- final String mimetype = bytes2UTF8(rs.getBytes("FileMimeType"));
- ret.fileType =
- java.util.Objects.equals("inode/directory", mimetype)
- ? ObjectType.DIRECTORY
- : (Objects.equal("inode/link", mimetype) ? ObjectType.LINK : ObjectType.FILE);
- if (ret.fileType == ObjectType.FILE) {
- ret.fileMimeType = mimetype;
- }
- ret.fileStorageId = bytes2UTF8(rs.getBytes("FileStorageID"));
- ret.fileKey = key;
- }
- }
-
- public static ArrayList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
- throws SQLException {
- final ArrayList<VerySparseEntity> ret = new ArrayList<VerySparseEntity>();
- while (rs.next()) {
- final VerySparseEntity vsp = new VerySparseEntity();
- vsp.id = rs.getInt("ParentID");
- vsp.name = bytes2UTF8(rs.getBytes("ParentName"));
- vsp.description = bytes2UTF8(rs.getBytes("ParentDescription"));
- vsp.role = bytes2UTF8(rs.getBytes("ParentRole"));
- vsp.acl = bytes2UTF8(rs.getBytes("ACL"));
- ret.add(vsp);
- }
- return ret;
- }
-
- public static <K extends EntityInterface> K parseEntityFromVerySparseEntity(
- final K entity, final VerySparseEntity vse) {
- entity.setId(new EntityID(vse.id));
- entity.setName(vse.name);
- entity.setRole(vse.role);
- entity.setDescription(vse.description);
- return entity;
- }
-
- public static void parseParentsFromVerySparseEntity(
- final EntityInterface entity, final List<VerySparseEntity> pars) {
- for (final VerySparseEntity vsp : pars) {
- final Parent p = new Parent(new RetrieveEntity(new EntityID(vsp.id)));
- p.setName(vsp.name);
- p.setDescription(vsp.description);
- entity.addParent(p);
- }
- }
-
- private static void replace(
- final Property p, final Map<EntityID, Property> domainMap, final boolean isHead) {
- // ... find the corresponding domain and replace it
- ReferenceValue ref;
- try {
- ref = ReferenceValue.parseReference(p.getValue());
- } catch (final Message e) {
- throw new RuntimeException("This should never happen.");
- }
- final EntityInterface replacement = domainMap.get(ref.getId());
- if (replacement == null) {
- if (isHead) {
- throw new NullPointerException("Replacement was null");
- }
- // entity has been deleted (we are processing properties of an old entity version)
- p.setValue(null);
- p.addWarning(
- new Message(
- "The referenced entity has been deleted in the mean time and is not longer available."));
- return;
- }
- if (replacement.isDescOverride()) {
- p.setDescOverride(true);
- p.setDescription(replacement.getDescription());
- }
- if (replacement.isNameOverride()) {
- p.setNameOverride(true);
- p.setName(replacement.getName());
- }
- if (replacement.isDatatypeOverride()) {
- p.setDatatypeOverride(true);
- p.setDatatype(replacement.getDatatype());
- }
- p.setProperties(replacement.getProperties());
- p.setStatementStatus(replacement.getStatementStatus());
- p.setValue(replacement.getValue());
- }
-
- public static void transformToDeepPropertyTree(
- final EntityInterface e, final List<Property> protoProperties) {
- // here we will store every domain we can find and we will index it by
- // its id.
- final Map<EntityID, Property> domainMap = new HashMap<>();
-
- // loop over all properties and collect the domains
- for (final Property p : protoProperties) {
- // if this is a domain it represents a deeper branch of the property
- // tree.
- if (p.getRole() == Role.Domain) {
- if (domainMap.containsKey(p.getId())) {
- // aggregate the multiple values.
- final Property domain = domainMap.get(p.getId());
- if (!(domain.getValue() instanceof CollectionValue)) {
- final SingleValue singleValue = (SingleValue) domain.getValue();
- final CollectionValue vals = new CollectionValue();
- final IndexedSingleValue iSingleValue =
- new IndexedSingleValue(domain.getPIdx(), singleValue);
- vals.add(iSingleValue);
- domain.setValue(vals);
- }
- ((CollectionValue) domain.getValue()).add(p.getPIdx(), p.getValue());
- } else {
- domainMap.put(p.getId(), p);
- }
- }
- }
-
- // loop over all properties
- final boolean isHead =
- e.getVersion().getSuccessors() == null || e.getVersion().getSuccessors().isEmpty();
- for (final Property p : protoProperties) {
-
- // if this is a replacement
- if (p.getStatementStatus() == StatementStatus.REPLACEMENT) {
- replace(p, domainMap, isHead);
- }
-
- for (final Property subP : p.getProperties()) {
- if (subP.getStatementStatus() == StatementStatus.REPLACEMENT) {
- replace(subP, domainMap, isHead);
- }
- }
-
- if (p.getId().equals(e.getId())) {
- // this is the value of an abstract property.
- e.setValue(p.getValue());
- } else if (p.getRole() != Role.Domain) {
- // if this is not a domain it is to be added to the properties
- // of e.
- e.addProperty(p);
- }
- }
- }
-
- public static ArrayList<Property> parseFromProtoProperties(final List<ProtoProperty> protos) {
- final ArrayList<Property> ret = new ArrayList<Property>();
- for (final ProtoProperty pp : protos) {
- final Property property = parseFlatProperty(pp.property);
- parseFromFlatProperties(property.getProperties(), pp.subProperties);
- ret.add(property);
- }
- return ret;
- }
-
- private static void parseFromFlatProperties(
- final List<Property> properties, final List<FlatProperty> props) {
- for (final FlatProperty fp : props) {
- final Property property = parseFlatProperty(fp);
- properties.add(property);
- }
- }
-
- private static Property parseFlatProperty(final FlatProperty fp) {
- final Property property = new Property(new RetrieveEntity());
- property.parseFlatProperty(fp);
- return property;
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
index ccadd6b17d5af0218d60db5f485a9bdd360f6509..d9dae7278ff1b8d74927e76ae9a47c9c52a589e2 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
@@ -47,8 +47,9 @@ import org.caosdb.server.entity.Message;
import org.caosdb.server.entity.RetrieveEntity;
import org.caosdb.server.entity.StatementStatus;
import org.caosdb.server.entity.wrapper.Property;
+import org.caosdb.server.filesystem.FileSystem.ObjectType;
import org.caosdb.server.filesystem.Hash;
-import org.caosdb.server.filesystem.Hasher;
+import org.caosdb.server.filesystem.Path;
public class DatabaseUtils {
@@ -229,14 +230,39 @@ public class DatabaseUtils {
ret.datatype_name = bytes2UTF8(rs.getBytes("DatatypeName"));
ret.collection = bytes2UTF8(rs.getBytes("Collection"));
- ret.filePath = bytes2UTF8(rs.getBytes("FilePath"));
- ret.fileSize = rs.getLong("FileSize");
- ret.fileHash = Hash.create(rs.getString("FileHash"), 0, Hasher.SHA512);
-
ret.versionId = bytes2UTF8(rs.getBytes("Version"));
+ parseFSODescriptorFields(rs, ret);
return ret;
}
+ public static void parseFSODescriptorFields(final ResultSet rs, final SparseEntity ret)
+ throws SQLException {
+ final String key = bytes2UTF8(rs.getBytes("FileKey"));
+ if (key != null) {
+ // ret.fileParentId = rs.getInt("FileParentID");
+ ret.filePath = new Path(bytes2UTF8(rs.getBytes("FilePath")));
+ ret.fileSize = rs.getLong("FileSize");
+ if (rs.wasNull()) {
+ ret.fileSize = null;
+ }
+ ret.fileHash =
+ Hash.create(
+ bytes2UTF8(rs.getBytes("FileHash")),
+ rs.getLong("FileHashChecked"),
+ bytes2UTF8(rs.getBytes("FileHashAlgo")));
+ final String mimetype = bytes2UTF8(rs.getBytes("FileMimeType"));
+ ret.fileType =
+ java.util.Objects.equals("inode/directory", mimetype)
+ ? ObjectType.DIRECTORY
+ : (Objects.equal("inode/link", mimetype) ? ObjectType.LINK : ObjectType.FILE);
+ if (ret.fileType == ObjectType.FILE) {
+ ret.fileMimeType = mimetype;
+ }
+ ret.fileStorageId = bytes2UTF8(rs.getBytes("FileStorageID"));
+ ret.fileKey = key;
+ }
+ }
+
public static LinkedList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
throws SQLException {
final LinkedList<VerySparseEntity> ret = new LinkedList<>();
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileEntityByPath.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileEntityByPath.java
index 54234d86ad9ab8029d9ed313caacd333ecd933b3..cbb7ea6030467e1c642a267474acced3153fc29a 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileEntityByPath.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileEntityByPath.java
@@ -25,7 +25,6 @@ package org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.GetFileEntityByPathImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -74,7 +73,7 @@ public class MySQLGetFileEntityByPath extends MySQLTransaction implements GetFil
try (ResultSet rs = stmt.executeQuery()) {
if (rs.next()) {
final SparseEntity ret = new SparseEntity();
- ret.id = rs.getInt("FileId");
+ ret.id = rs.getString("FileId");
DatabaseUtils.parseFSODescriptorFields(rs, ret);
return ret;
} else {
@@ -86,7 +85,7 @@ public class MySQLGetFileEntityByPath extends MySQLTransaction implements GetFil
private SparseEntity retrieveEntityACL(final SparseEntity entity)
throws SQLException, ConnectionException {
final PreparedStatement stmt = prepareStatement(STMT_GET_ACL);
- stmt.setInt(1, entity.id);
+ stmt.setString(1, entity.id);
try (ResultSet rs = stmt.executeQuery()) {
rs.next();
entity.acl = DatabaseUtils.bytes2UTF8(rs.getBytes("ACL"));
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
deleted file mode 100644
index 33f6bacfd29e0c1999d3a4681f5daa45d1a59c5b..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero 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 Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- */
-package org.caosdb.server.database.backend.implementation.MySQL;
-
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.filesystem.Hash;
-import org.caosdb.server.filesystem.Hasher;
-
-/**
- * Retrieve the entity id of a file with the given path (or null).
- *
- * @author Timm Fitschen <t.fitschen@indiscale.com>
- */
-public class MySQLGetFileRecordByPath extends MySQLTransaction implements GetFileRecordByPathImpl {
-
- public MySQLGetFileRecordByPath(final Access access) {
- super(access);
- }
-
- public static final String STMT_GET_ID_BY_PATH =
- "SELECT (Select id from entity_ids WHERE internal_id = files.file_id) as entity_id, size, hex(hash) AS file_hash, checked_timestamp FROM files WHERE path=?";
-
- @Override
- public SparseEntity execute(final String path) throws TransactionException {
- try {
- final PreparedStatement stmt = prepareStatement(STMT_GET_ID_BY_PATH);
-
- stmt.setString(1, path);
- final ResultSet rs = stmt.executeQuery();
- try {
- if (rs.next()) {
- final SparseEntity ret = new SparseEntity();
- ret.id = rs.getString("entity_id");
- ret.fileSize = rs.getLong("size");
- ret.fileChecked = rs.getLong("checked_timestamp");
- ret.fileHash = Hash.create(rs.getString("file_hash"), 0, Hasher.SHA512);
- return ret;
- } else {
- return null;
- }
- } finally {
- rs.close();
- }
- } catch (final SQLException e) {
- throw new TransactionException(e);
- } catch (final ConnectionException e) {
- throw new TransactionException(e);
- }
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFilesInDirectory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFilesInDirectory.java
index 05eb01e2856e1af061b8f884dad4e7cd75469ce5..cd743d5ed9d37271d53fd86af69a2ec6303b3e87 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFilesInDirectory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFilesInDirectory.java
@@ -5,7 +5,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.SparseEntity;
@@ -25,12 +24,12 @@ public class MySQLGetFilesInDirectory extends MySQLTransaction
public List<SparseEntity> execute(final EntityID directory_id) {
try {
final PreparedStatement stmt = prepareStatement(STMT_GET_FILES_IN_DIR);
- stmt.setInt(1, directory_id.toInteger());
+ stmt.setString(1, directory_id.toString());
final List<SparseEntity> result = new LinkedList<>();
try (ResultSet rs = stmt.executeQuery()) {
while (rs.next()) {
final SparseEntity entity = new SparseEntity();
- entity.id = rs.getInt("FileId");
+ entity.id = rs.getString("FileId");
DatabaseUtils.parseFSODescriptorFields(rs, entity);
result.add(entity);
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetVirtualFSO.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetVirtualFSO.java
index 71b0ba1e99789e9fd08d7d1ca5abd5639baf2939..e2b1331f814396259af3a37858ad2318da9defbf 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetVirtualFSO.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetVirtualFSO.java
@@ -3,7 +3,6 @@ package org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.GetVirtualFSOImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -18,7 +17,7 @@ public class MySQLGetVirtualFSO extends MySQLTransaction implements GetVirtualFS
}
public static final String STMT_GET_FSO =
- "SELECT 'SHA-512' AS FileHashAlgo, file_id AS FileId, "
+ "SELECT 'SHA-512' AS FileHashAlgo, (SELECT id FROM entity_ids WHERE internal_id = file_id LIMIT 1) AS FileId, "
+ /*parent_directory AS FileParentID,*/ " path AS FilePath, size AS FileSize, hex(hash) AS FileHash, checked_timestamp AS FileHashChecked, mimetype AS FileMimeType, file_storage_id AS FileStorageID, file_key AS FileKey FROM files WHERE file_storage_id = ? AND file_key = ?";
@Override
@@ -30,7 +29,7 @@ public class MySQLGetVirtualFSO extends MySQLTransaction implements GetVirtualFS
ResultSet resultSet = stmt.executeQuery();
if (resultSet.next()) {
SparseEntity e = new SparseEntity();
- e.id = resultSet.getInt("FileId");
+ e.id = resultSet.getString("FileId");
DatabaseUtils.parseFSODescriptorFields(resultSet, e);
return new FSODescriptor(e);
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertFSODescriptor.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertFSODescriptor.java
index f12f6a4488726862f787ab7dbc0bf6a2e7697411..6f3cdc7a955dd8528d5e5cb628599e21256e8981 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertFSODescriptor.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertFSODescriptor.java
@@ -24,7 +24,7 @@ public class MySQLInsertFSODescriptor extends MySQLTransaction implements Insert
try {
final PreparedStatement insertFilePropsStmt = prepareStatement(STMT_INSERT_FILE_PROPERTIES);
if (entity.filePath != null) {
- insertFilePropsStmt.setInt(1, entity.id);
+ insertFilePropsStmt.setString(1, entity.id);
if (entity.fileHash != null) {
insertFilePropsStmt.setString(2, entity.fileHash.value);
insertFilePropsStmt.setString(3, entity.fileHash.algorithm);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
index b752abd0d16d759d796dada00610ec039588f71a..345dc5e91ecb83bd4e5f07817d3dce3200704cc7 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
@@ -24,7 +24,6 @@ package org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListFiles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListFiles.java
index 504f992a8fc26cccea4c93eb6970c6e7655ab2d7..72d8365f2d6cc69b10b91e8c1e48d3e0f0333d89 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListFiles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListFiles.java
@@ -5,7 +5,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.ListFilesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -40,7 +39,7 @@ public class MySQLListFiles extends MySQLTransaction implements ListFilesImpl {
try (ResultSet rs = stmt.executeQuery()) {
while (rs.next()) {
final SparseEntity entity = new SparseEntity();
- entity.id = rs.getInt("FileId");
+ entity.id = rs.getString("FileId");
DatabaseUtils.parseFSODescriptorFields(rs, entity);
result.add(new FSODescriptor(entity));
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
index 887b1ed5128277582299750d39ae50ade2e5764a..036a9b4fbcd6b0f6489988441a5b2df45d7a7c23 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
@@ -74,9 +74,9 @@ public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateS
updateFilePropsStmt.setString(7, spe.fileStorageId); // FileStorageId
updateFilePropsStmt.setString(8, spe.fileKey); // FileKey
if (spe.fileParentId != null) {
- updateFilePropsStmt.setInt(9, spe.fileParentId);
+ updateFilePropsStmt.setString(9, spe.fileParentId);
} else {
- updateFilePropsStmt.setNull(9, Types.INTEGER); // FileParentDirectory
+ updateFilePropsStmt.setNull(9, Types.VARCHAR); // FileParentDirectory
}
} else {
// move file to archive
diff --git a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java b/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
index 22bcf045603fd020d6d47334689327c93e9aa7dc..94c875ceb4d01c5f1fa6f8feb9e0e1f99cc461d5 100644
--- a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
@@ -46,7 +46,7 @@ public class SparseEntity extends VerySparseEntity {
public String fileStorageId = null;
public String fileKey = null;
public String fileMimeType = null;
- public Integer fileParentId;
+ public String fileParentId;
public FileSystem.ObjectType fileType = ObjectType.FILE;
public String versionId = null;
public Long versionSeconds = null;
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index cf7bbecc7dfa324a61b66ebe44cb94118c295b4b..20d86fcc48e0cb3fb1c9c51efc982ead9fa1bb09 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -392,7 +392,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
ret.fileStorageId = getFSODescriptor().getFileStorageId();
ret.fileKey = getFSODescriptor().getKey();
if (getFSODescriptor().getParentDirectoryID() != null) {
- ret.fileParentId = getFSODescriptor().getParentDirectoryID().toInteger();
+ ret.fileParentId = getFSODescriptor().getParentDirectoryID().toString();
}
}
return ret;
diff --git a/src/main/java/org/caosdb/server/filesystem/FSODescriptor.java b/src/main/java/org/caosdb/server/filesystem/FSODescriptor.java
index 1949c31d558ac44d1e48937a551bb346108cf90e..212b35ace3f8cc33f79f8420a5e68aaecd939437 100644
--- a/src/main/java/org/caosdb/server/filesystem/FSODescriptor.java
+++ b/src/main/java/org/caosdb/server/filesystem/FSODescriptor.java
@@ -79,7 +79,7 @@ public class FSODescriptor implements VirtualFSODescriptorInterface {
this.key = spe.fileKey;
this.type = spe.fileType;
this.mimeType = spe.fileMimeType;
- this.parentDirectory = new EntityID(spe.fileParentId);
+ // this.parentDirectory = new EntityID(spe.fileParentId);
}
public FSODescriptor(final Path path, final Long size) {
diff --git a/src/main/java/org/caosdb/server/resource/FileSystemResource.java b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
index ddfbc5acf976faee5471b884b0af2282edd3e15c..66ee11bcd29e8533660283d1649e0ae67ce4afa2 100644
--- a/src/main/java/org/caosdb/server/resource/FileSystemResource.java
+++ b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
@@ -131,7 +131,7 @@ public class FileSystemResource extends AbstractCaosDBServerResource {
throw new UnsupportedOperationException(
"Unknown FileSystem.ObjectType: " + child.getObjectType().toString());
}
- if (child.getEntityId().toInteger() != null) {
+ if (child.getEntityId().toString() != null) {
celem.setAttribute("id", child.getEntityId().toString());
}
diff --git a/src/test/java/org/caosdb/server/database/backend/transaction/BackendTransactionTest.java b/src/test/java/org/caosdb/server/database/backend/transaction/BackendTransactionTest.java
index e0cb425a25ed4d3c27e1cdbb610607077ed0fb92..0ea5f871925524bba650cc47a63d717e6b2f8437 100644
--- a/src/test/java/org/caosdb/server/database/backend/transaction/BackendTransactionTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/transaction/BackendTransactionTest.java
@@ -19,7 +19,7 @@ public class BackendTransactionTest {
final BackendTransaction transaction = new InsertTransactionHistory(null, null, null, null);
assertEquals("Retrieve", transaction.getTransactionType(new RetrieveEntity("test")));
assertEquals("Insert", transaction.getTransactionType(new InsertEntity("test", Role.Record)));
- assertEquals("Delete", transaction.getTransactionType(new DeleteEntity(new EntityID(1234))));
+ assertEquals("Delete", transaction.getTransactionType(new DeleteEntity(new EntityID("1234"))));
assertEquals("Update", transaction.getTransactionType(new UpdateEntity(new Element("Record"))));
}
}