Merge branch 'dev' into f-one-time-tokens

.gitlab-ci.yml

@@ -23,6 +23,7 @@
 #
 
 variables:
+  DEPLOY_REF: dev
   CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/caosdb-server/caosdb-server-testenv:latest
 
 image: $CI_REGISTRY_IMAGE
@@ -69,7 +70,8 @@ trigger_build:
   script:
     - /usr/bin/curl -X POST
       -F token=$DEPLOY_TRIGGER_TOKEN
+      -F "variables[F_BRANCH]=$CI_COMMIT_REF_NAME"
       -F "variables[SERVER]=$CI_COMMIT_REF_NAME"
       -F "variables[TriggerdBy]=SERVER"
       -F "variables[TriggerdByHash]=$CI_COMMIT_SHORT_SHA"
-      -F ref=dev https://gitlab.indiscale.com/api/v4/projects/14/trigger/pipeline
+      -F ref=$DEPLOY_REF https://gitlab.indiscale.com/api/v4/projects/14/trigger/pipeline

CHANGELOG.md

@@ -36,10 +36,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* #51 - name queries (e.g. `FIND ENTITY WITH name = ...`)
 - #27 - star matches slashes (e.g. for `FIND ... STORED AT /*.dat`).
 - #30 - file path cannot be in quotes
-- #46 - Server-side scripting failed as an unprivileged user because the was no
-  writable home directory.
+- #46 - Server-side scripting failed as an unprivileged user because there was
+  no writable home directory.
 - NaN Double Values (see #41)
 - #14 - Handle files on file system without File entity: Those entries are
   returned without ID but with a notice now.
@@ -49,7 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Security (in case of vulnerabilities)
 
 - TLS is by default restricted to v1.2 and v1.3 now.
-- #11 - `pam_authentication` and `ldap_authentication.sh` leaked the password to unprivileged
+- #11 - PAM and LDAP authentication no longer leak the password to unprivileged
   processes on the same machine.
 - #68 - Shadow sensitive information when logging for debugging purposes.
 

conf/core/server.conf

@@ -67,7 +67,7 @@ MYSQL_USER_NAME=caosdb
 # Password for the user
 MYSQL_USER_PASSWORD=caosdb
 # Schema of mysql procedures and tables which is required by this CaosDB instance
-MYSQL_SCHEMA_VERSION=v2.1.2
+MYSQL_SCHEMA_VERSION=v3.0.0-rc1
 
 
 # --------------------------------------------------

pom.xml

@@ -125,7 +125,7 @@
     <dependency>
       <groupId>org.antlr</groupId>
       <artifactId>antlr4</artifactId>
-      <version>4.7.2</version>
+      <version>4.8-1</version>
     </dependency>
     <dependency>
       <groupId>org.restlet.jse</groupId>
@@ -222,7 +222,7 @@
       <plugin>
         <groupId>org.antlr</groupId>
         <artifactId>antlr4-maven-plugin</artifactId>
-        <version>4.7.2</version>
+        <version>4.8-1</version>
         <configuration>
           <sourceDirectory>${basedir}/src/main/java</sourceDirectory>
         </configuration>

src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java

@@ -18,8 +18,12 @@ public class MySQLGetAllNames extends MySQLTransaction implements GetAllNamesImp
     super(access);
   }
 
+  /** Retrieve tuples (EntityName, EntityRole, ACL) for all entities which have a name. */
   public static final String STMT_GET_ALL_NAMES =
-      "Select e.name as EntityName, e.role as EntityRole, a.acl as ACL FROM entities as e JOIN entity_acl as a ON (a.id=e.acl) WHERE e.name IS NOT NULL and e.role!='ROLE'";
+      "SELECT d.value as EntityName, e.role AS EntityRole, a.acl AS ACL "
+          + "FROM name_data AS d JOIN entities AS e JOIN entity_acl AS a "
+          + "ON (d.domain_id = 0 AND d.property_id = 20 AND d.entity_id = e.id AND a.id = e.acl) "
+          + "WHERE e.role != 'ROLE' AND e.role != 'DATATYPE'";
 
   @Override
   public List<SparseEntity> execute() {

src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java

@@ -36,9 +36,19 @@ public class MySQLGetIDByName extends MySQLTransaction implements GetIDByNameImp
     super(access);
   }
 
-  public static final String STMT_GET_ID_BY_NAME = "Select id from entities where name=?";
-  public static final String STMT_AND_ROLE = " AND role=?";
-  public static final String STMT_NOT_ROLE = " AND role!='ROLE'";
+  /**
+   * Resolves the (primary) name of an entity to an id. This query is not necessarily unique.
+   * Therefore {@link #STMT_AND_ROLE}, {@link #STMT_NOT_ROLE}, and {@link #STMT_LIMIT} can as
+   * additional conditions.
+   */
+  public static final String STMT_GET_ID_BY_NAME =
+      "Select n.entity_id AS id "
+          + "FROM name_data AS n JOIN entities AS e "
+          + "ON (n.domain_id=0 AND n.property_id=20 AND e.id = n.entity_id)"
+          + "WHERE n.value=?";
+
+  public static final String STMT_AND_ROLE = " AND e.role=?";
+  public static final String STMT_NOT_ROLE = " AND e.role!='ROLE'";
   public static final String STMT_LIMIT = " LIMIT ";
 
   @Override
@@ -55,17 +65,13 @@ public class MySQLGetIDByName extends MySQLTransaction implements GetIDByNameImp
       if (role != null) {
         stmt.setString(2, role);
       }
-      ResultSet rs = null;
-      try {
-        rs = stmt.executeQuery();
+      try (ResultSet rs = stmt.executeQuery()) {
         final ArrayList<Integer> ret = new ArrayList<Integer>();
         while (rs.next()) {
           ret.add(rs.getInt("id"));
         }
 
         return ret;
-      } finally {
-        rs.close();
       }
     } catch (final Exception e) {
       throw new TransactionException(e);

src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java

@@ -15,10 +15,22 @@ public class MySQLInsertEntityDatatype extends MySQLTransaction
     super(access);
   }
 
+  /**
+   * Inserts atomic data types of properties into the data_type table. Has two parameters, the
+   * property_id and the data type name.
+   */
   public static final String STMT_INSERT_ENTITY_DATATYPE =
-      "INSERT INTO data_type (domain_id, entity_id, property_id, datatype) SELECT 0, 0, ?, ( SELECT id from entities where name = ? LIMIT 1);";
+      "INSERT INTO data_type (domain_id, entity_id, property_id, datatype) "
+          + "SELECT 0, 0, ?, "
+          + "( SELECT entity_id FROM name_data WHERE domain_id = 0 AND property_id = 20 AND value = ? LIMIT 1);";
+
+  /**
+   * Inserts collection data types of properties into the data_type table. Has two parameters, the
+   * property_id and the type of collection (e.g. 'LIST').
+   */
   public static final String STMT_INSERT_ENTITY_COLLECTION =
-      "INSERT INTO collection_type (domain_id, entity_id, property_id, collection) SELECT 0, 0, ?, ?;";
+      "INSERT INTO collection_type (domain_id, entity_id, property_id, collection) "
+          + "SELECT 0, 0, ?, ?;";
 
   @Override
   public void execute(final SparseEntity entity) {

src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java

@@ -38,17 +38,17 @@ public class MySQLRetrieveAll extends MySQLTransaction implements RetrieveAllImp
     super(access);
   }
 
-  public static final String STMT_GET_ALL_HEAD = "Select id from entities where ";
+  public static final String STMT_GET_ALL_HEAD = "Select id from entities where id > 99";
   public static final String STMT_ENTITY_WHERE_CLAUSE =
-      " ( role=? OR role='"
+      " AND ( role=? OR role='"
           + Role.RecordType
           + "' OR role='"
           + Role.Property
           + "' OR role='"
           + Role.File
           + "'"
-          + " ) AND ( NOT name=role OR name IS NULL)";
-  public static final String STMT_OTHER_ROLES = " role=? AND ( NOT name=role OR name IS NULL)";
+          + " )";
+  public static final String STMT_OTHER_ROLES = " AND role=?";
 
   @Override
   public List<Integer> execute(final String role) throws TransactionException {

src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java

@@ -38,8 +38,19 @@ public class MySQLRetrieveDatatypes extends MySQLTransaction implements Retrieve
     super(access);
   }
 
+  /**
+   * Retrieve (ParentID, ParentName, ParentDescription, ParentRole, ACL) tuple which actually
+   * contains the ID, name, description, role and ACL of the datatype. The misleading names should
+   * be fixed sometimes (TODO) but this also requires to adjust the code below, which uses {@link
+   * DatabaseUtils#parseParentResultSet(ResultSet)}.
+   */
   private static final String STMT_GET_DATATYPE =
-      "select id AS ParentID, name AS ParentName, description as ParentDescription, role as ParentRole, (SELECT acl FROM entity_acl as a WHERE a.id=e.acl) as ACL from entities as e where e.role='DATATYPE'";
+      "SELECT id AS ParentID, "
+          + "(SELECT value FROM name_data WHERE domain_id = 0 AND entity_ID = e.id AND property_id = 20) AS ParentName, "
+          + "description AS ParentDescription, "
+          + "role AS ParentRole, "
+          + "(SELECT acl FROM entity_acl AS a WHERE a.id=e.acl) as ACL "
+          + "FROM entities AS e WHERE e.role='DATATYPE'";
 
   @Override
   public ArrayList<VerySparseEntity> execute() throws TransactionException {

src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java

@@ -51,13 +51,10 @@ public class MySQLRetrieveSparseEntity extends MySQLTransaction
       final PreparedStatement preparedStatement = prepareStatement(stmtStr);
 
       preparedStatement.setInt(1, id);
-      final ResultSet rs = preparedStatement.executeQuery();
-      try {
+      try (final ResultSet rs = preparedStatement.executeQuery()) {
         if (rs.next()) {
           return DatabaseUtils.parseEntityResultSet(rs);
         }
-      } finally {
-        rs.close();
       }
     } catch (final SQLException e) {
       throw new TransactionException(e);