diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cf8544c1782b0d775cb6cec5694167219ec47e9b..8587b4072e1d7485406cd432aff9034e6c2e6b84 100644
--- a/.gitlab-ci.yml
+++ b/.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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 78cb02fb40b0313ab7e3274a38880dddcbccc14c..88ac0b5297a401ebcc3edda414cce13d3142d3fd 100644
--- a/CHANGELOG.md
+++ b/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.
diff --git a/conf/core/server.conf b/conf/core/server.conf
index e8281657dd1c9a7aa92bd94c7c974e93b0fee5c4..4c64ace935318b0bb8dc3ac13e16c9c4d7eb7c1c 100644
--- a/conf/core/server.conf
+++ b/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
# --------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 42279be9f3be99fb3d2d7d316e8549901aadeba8..0594c0548331f0e834fc0bc10a61fec69ffa9a69 100644
--- a/pom.xml
+++ b/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>
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
index d7c641cadebcde93b97187aa7a0ea2ded72d4678..060cf9b8a77ad15e430b34f06e2b17737dd27cc2 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
+++ b/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() {
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
index ff6d2b53d4e142cd634848d1c2edbccbe30892ad..e9797640d98b6e9f2afb2b95ff3ea5103b623070 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
+++ b/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);
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
index a2682e80b1997b53496e3ac2f8e6147726fb77c9..47671864570c1a041b8b164a0f045fbf70b47987 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
+++ b/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) {
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
index b93615ea529291b967ef1fc22206b8d953e408d0..7ae921315f55e94994a2868d5b0a9b8d8406542b 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
index 1c7609cc5ddf4eaff9bf2c742b43dd2bd27b0337..a8e12672cf21592c23d8cea0aa22629b4b68855c 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
index 749b0b91455c9f429821bbabce3aa99375a417cd..2aff2aaedda70672eb676597a2e3ba7a1db14352 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
+++ b/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);