feat: add option to disable OCR (#768)

fixes #344
refs #767

.github/workflows/build-deploy.yml

@@ -0,0 +1,84 @@
+name: Maven CI/CD
+
+on:
+  push:
+    branches: [master]
+    tags: [v*]
+  workflow_dispatch:
+
+jobs:
+  build_and_publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: "11"
+          distribution: "temurin"
+          cache: maven
+      - name: Install test dependencies
+        run: sudo apt-get update && sudo apt-get -y -q --no-install-recommends install ffmpeg mediainfo tesseract-ocr tesseract-ocr-deu
+      - name: Build with Maven
+        run: mvn --batch-mode -Pprod clean install
+      - name: Upload war artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: docs-web-ci.war
+          path: docs-web/target/docs*.war
+
+  build_docker_image:
+    name: Publish to Docker Hub
+    runs-on: ubuntu-latest
+    needs: [build_and_publish]
+
+    steps:
+      - 
+        name: Checkout
+        uses: actions/checkout@v2
+      - 
+        name: Download war artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: docs-web-ci.war
+          path: docs-web/target
+      - 
+        name: Setup up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - 
+        name: Login to DockerHub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - 
+        name: Populate Docker metadata
+        id: metadata
+        uses: docker/metadata-action@v3
+        with:
+          images: sismics/docs
+          flavor: |
+            latest=false
+          tags: |
+            type=ref,event=tag
+            type=raw,value=latest,enable=${{ github.ref_type != 'tag' }}
+          labels: |
+            org.opencontainers.image.title = Teedy
+            org.opencontainers.image.description = Teedy is an open source, lightweight document management system for individuals and businesses.
+            org.opencontainers.image.created = ${{ github.event_created_at }}
+            org.opencontainers.image.author = Sismics
+            org.opencontainers.image.url = https://teedy.io/
+            org.opencontainers.image.vendor = Sismics
+            org.opencontainers.image.license = GPLv2
+            org.opencontainers.image.version = ${{ github.event_head_commit.id }}
+      - 
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.metadata.outputs.tags }}
+          labels: ${{ steps.metadata.outputs.labels }}

.gitignore

@@ -13,4 +13,9 @@ node_modules
 import_test
 teedy-importer-linux
 teedy-importer-macos
-teedy-importer-win.exe
+teedy-importer-win.exe
+docs/*
+!docs/.gitkeep
+
+#macos
+.DS_Store

Dockerfile

@@ -1,12 +1,26 @@
-FROM sismics/ubuntu-jetty:9.4.36
+FROM ubuntu:22.04
 LABEL maintainer="b.gamard@sismics.com"
 
+# Run Debian in non interactive mode
+ENV DEBIAN_FRONTEND noninteractive
+
+# Configure env
+ENV LANG C.UTF-8
+ENV LC_ALL C.UTF-8
+ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
+ENV JAVA_OPTIONS -Dfile.encoding=UTF-8 -Xmx1g
+ENV JETTY_VERSION 11.0.20
+ENV JETTY_HOME /opt/jetty
+
+# Install packages
 RUN apt-get update && \
     apt-get -y -q --no-install-recommends install \
+    vim less procps unzip wget tzdata openjdk-11-jdk \
     ffmpeg \
     mediainfo \
     tesseract-ocr \
     tesseract-ocr-ara \
+    tesseract-ocr-ces \
     tesseract-ocr-chi-sim \
     tesseract-ocr-chi-tra \
     tesseract-ocr-dan \
@@ -30,13 +44,32 @@ RUN apt-get update && \
     tesseract-ocr-tha \
     tesseract-ocr-tur \
     tesseract-ocr-ukr \
-    tesseract-ocr-vie && \
+    tesseract-ocr-vie \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
+    tesseract-ocr-sqi \
+    && apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+RUN dpkg-reconfigure -f noninteractive tzdata
 
-# Remove the embedded javax.mail jar from Jetty
+# Install Jetty
-RUN rm -f /opt/jetty/lib/mail/javax.mail.glassfish-*.jar
+RUN wget -nv -O /tmp/jetty.tar.gz \
+    "https://repo1.maven.org/maven2/org/eclipse/jetty/jetty-home/${JETTY_VERSION}/jetty-home-${JETTY_VERSION}.tar.gz" \
+    && tar xzf /tmp/jetty.tar.gz -C /opt \
+    && mv /opt/jetty* /opt/jetty \
+    && useradd jetty -U -s /bin/false \
+    && chown -R jetty:jetty /opt/jetty \
+    && mkdir /opt/jetty/webapps \
+    && chmod +x /opt/jetty/bin/jetty.sh
 
-ADD docs.xml /opt/jetty/webapps/docs.xml
+EXPOSE 8080
-ADD docs-web/target/docs-web-*.war /opt/jetty/webapps/docs.war
 
-ENV JAVA_OPTIONS -Xmx1g
+# Install app
+RUN mkdir /app && \
+    cd /app && \
+    java -jar /opt/jetty/start.jar --add-modules=server,http,webapp,deploy
+
+ADD docs.xml /app/webapps/docs.xml
+ADD docs-web/target/docs-web-*.war /app/webapps/docs.war
+
+WORKDIR /app
+
+CMD ["java", "-jar", "/opt/jetty/start.jar"]

README.md

@@ -3,6 +3,7 @@
 </h3>
 
 [![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
+[![Maven CI/CD](https://github.com/sismics/docs/actions/workflows/build-deploy.yml/badge.svg)](https://github.com/sismics/docs/actions/workflows/build-deploy.yml)
 
 Teedy is an open source, lightweight document management system for individuals and businesses.
 
@@ -14,8 +15,7 @@ Teedy is an open source, lightweight document management system for individuals
 
 ![New!](https://teedy.io/img/laptop-demo.png?20180301)
 
-Demo
+# Demo
-----
 
 A demo is available at [demo.teedy.io](https://demo.teedy.io)
 
@@ -23,8 +23,7 @@ A demo is available at [demo.teedy.io](https://demo.teedy.io)
 - "admin" login with "admin" password
 - "demo" login with "password" password 
 
-Features
+# Features
---------
 
 - Responsive user interface
 - Optical character recognition
@@ -54,21 +53,20 @@ Features
 - [Bulk files importer](https://github.com/sismics/docs/tree/master/docs-importer) (single or scan mode)
 - Tested to one million documents
 
-Install with Docker
+# Install with Docker
--------------------
 
-A preconfigured Docker image is available, including OCR and media conversion tools, listening on port 8080. The database is an embedded H2 database but PostgreSQL is also supported for more performance.
+A preconfigured Docker image is available, including OCR and media conversion tools, listening on port 8080. If no PostgreSQL config is provided, the database is an embedded H2 database. The H2 embedded database should only be used for testing. For production usage use the provided PostgreSQL configuration (check the Docker Compose example)
 
 **The default admin password is "admin". Don't forget to change it before going to production.**
 
 - Master branch, can be unstable. Not recommended for production use: `sismics/docs:latest`
-- Latest stable version: `sismics/docs:v1.10`
+- Latest stable version: `sismics/docs:v1.11`
 
 The data directory is `/data`. Don't forget to mount a volume on it.
 
 To build external URL, the server is expecting a `DOCS_BASE_URL` environment variable (for example https://teedy.mycompany.com)
 
-### Available environment variables
+## Available environment variables
 
 - General
   - `DOCS_BASE_URL`: The base url used by the application. Generated url's will be using this as base.
@@ -83,6 +81,7 @@ To build external URL, the server is expecting a `DOCS_BASE_URL` environment var
   - `DATABASE_URL`: The jdbc connection string to be used by `hibernate`.
   - `DATABASE_USER`: The user which should be used for the database connection.
   - `DATABASE_PASSWORD`: The password to be used for the database connection.
+  - `DATABASE_POOL_SIZE`: The pool size to be used for the database connection.
 
 - Language
   - `DOCS_DEFAULT_LANGUAGE`: The language which will be used as default. Currently supported values are:
@@ -94,41 +93,19 @@ To build external URL, the server is expecting a `DOCS_BASE_URL` environment var
   - `DOCS_SMTP_USERNAME`: The username to be used.
   - `DOCS_SMTP_PASSWORD`: The password to be used.
 
-### Examples
+## Examples
 
 In the following examples some passwords are exposed in cleartext. This was done in order to keep the examples simple. We strongly encourage you to use variables with an `.env` file or other means to securely store your passwords.
 
-#### Using the internal database
+
+### Default, using PostgreSQL
 
 ```yaml
 version: '3'
 services:
 # Teedy Application
   teedy-server:
-    image: sismics/docs:v1.10
+    image: sismics/docs:v1.11
-    restart: unless-stopped
-    ports:
-      # Map internal port to host
-      - 8080:8080
-    environment:
-      # Base url to be used
-      DOCS_BASE_URL: "https://docs.example.com"
-      # Set the admin email
-      DOCS_ADMIN_EMAIL_INIT: "admin@example.com"
-      # Set the admin password (in this example: "superSecure")
-      DOCS_ADMIN_PASSWORD_INIT: "$$2a$$05$$PcMNUbJvsk7QHFSfEIDaIOjk1VI9/E7IPjTKx.jkjPxkx2EOKSoPS"
-    volumes:
-      - ./docs/data:/data
-```
-
-#### Using PostgreSQL
-
-```yaml
-version: '3'
-services:
-# Teedy Application
-  teedy-server:
-    image: sismics/docs:v1.10
     restart: unless-stopped
     ports:
       # Map internal port to host
@@ -146,6 +123,7 @@ services:
       DATABASE_URL: "jdbc:postgresql://teedy-db:5432/teedy"
       DATABASE_USER: "teedy_db_user"
       DATABASE_PASSWORD: "teedy_db_password"
+      DATABASE_POOL_SIZE: "10"
     volumes:
       - ./docs/data:/data
     networks:
@@ -179,10 +157,32 @@ networks:
     driver: bridge
 ```
 
-Manual installation
+### Using the internal database (only for testing)
--------------------
 
-#### Requirements
+```yaml
+version: '3'
+services:
+# Teedy Application
+  teedy-server:
+    image: sismics/docs:v1.11
+    restart: unless-stopped
+    ports:
+      # Map internal port to host
+      - 8080:8080
+    environment:
+      # Base url to be used
+      DOCS_BASE_URL: "https://docs.example.com"
+      # Set the admin email
+      DOCS_ADMIN_EMAIL_INIT: "admin@example.com"
+      # Set the admin password (in this example: "superSecure")
+      DOCS_ADMIN_PASSWORD_INIT: "$$2a$$05$$PcMNUbJvsk7QHFSfEIDaIOjk1VI9/E7IPjTKx.jkjPxkx2EOKSoPS"
+    volumes:
+      - ./docs/data:/data
+```
+
+# Manual installation
+
+## Requirements
 
 - Java 11
 - Tesseract 4 for OCR
@@ -190,13 +190,12 @@ Manual installation
 - mediainfo for video metadata extraction
 - A webapp server like [Jetty](http://eclipse.org/jetty/) or [Tomcat](http://tomcat.apache.org/)
 
-#### Download
+## Download
 
 The latest release is downloadable here: <https://github.com/sismics/docs/releases> in WAR format. 
 **The default admin password is "admin". Don't forget to change it before going to production.**
 
-How to build Teedy from the sources
+## How to build Teedy from the sources
-----------------------------------
 
 Prerequisites: JDK 11, Maven 3, NPM, Grunt, Tesseract 4
 
@@ -209,35 +208,39 @@ Teedy is organized in several Maven modules:
 First off, clone the repository: `git clone git://github.com/sismics/docs.git`
 or download the sources from GitHub.
 
-#### Launch the build
+### Launch the build
 
 From the root directory:
 
-    mvn clean -DskipTests install
+```console
+mvn clean -DskipTests install
+```
 
-#### Run a stand-alone version
+### Run a stand-alone version
 
 From the `docs-web` directory:
 
-    mvn jetty:run
+```console
+mvn jetty:run
+```
 
-#### Build a .war to deploy to your servlet container
+### Build a .war to deploy to your servlet container
 
 From the `docs-web` directory:
 
-    mvn -Pprod -DskipTests clean install
+```console
+mvn -Pprod -DskipTests clean install
+```
 
 You will get your deployable WAR in the `docs-web/target` directory.
 
-Contributing
+# Contributing
-------------
 
 All contributions are more than welcomed. Contributions may close an issue, fix a bug (reported or not reported), improve the existing code, add new feature, and so on.
 
 The `master` branch is the default and base branch for the project. It is used for development and all Pull Requests should go there.
 
-License
+# License
--------
 
 Teedy is released under the terms of the GPL license. See `COPYING` for more
 information or see <http://opensource.org/licenses/GPL-2.0>.

docker-compose.yml

@@ -0,0 +1,18 @@
+version: '3'
+services:
+# Teedy Application
+  teedy-server:
+    image: sismics/docs:v1.10
+    restart: unless-stopped
+    ports:
+      # Map internal port to host
+      - 8080:8080
+    environment:
+      # Base url to be used
+      DOCS_BASE_URL: "https://docs.example.com"
+      # Set the admin email
+      DOCS_ADMIN_EMAIL_INIT: "admin@example.com"
+      # Set the admin password (in this example: "superSecure")
+      DOCS_ADMIN_PASSWORD_INIT: "$$2a$$05$$PcMNUbJvsk7QHFSfEIDaIOjk1VI9/E7IPjTKx.jkjPxkx2EOKSoPS"
+    volumes:
+      - ./docs/data:/data

docs-core/pom.xml

@@ -5,10 +5,10 @@
   <parent>
     <groupId>com.sismics.docs</groupId>
     <artifactId>docs-parent</artifactId>
-    <version>1.10</version>
+    <version>1.12-SNAPSHOT</version>
-    <relativePath>..</relativePath>
+    <relativePath>../pom.xml</relativePath>
   </parent>
-  
+
   <modelVersion>4.0.0</modelVersion>
   <artifactId>docs-core</artifactId>
   <packaging>jar</packaging>
@@ -17,20 +17,10 @@
   <dependencies>
     <!-- Persistence layer dependencies -->
     <dependency>
-      <groupId>org.hibernate</groupId>
+      <groupId>org.hibernate.orm</groupId>
       <artifactId>hibernate-core</artifactId>
     </dependency>
-    
+
-    <dependency>
-      <groupId>org.hibernate</groupId>
-      <artifactId>hibernate-entitymanager</artifactId>
-    </dependency>
-    
-    <dependency>
-      <groupId>org.hibernate</groupId>
-      <artifactId>hibernate-c3p0</artifactId>
-    </dependency>
-    
     <!-- Other external dependencies -->
     <dependency>
       <groupId>joda-time</groupId>
@@ -41,30 +31,30 @@
       <groupId>com.google.guava</groupId>
       <artifactId>guava</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-compress</artifactId>
     </dependency>
-    
+
     <dependency>
-      <groupId>commons-lang</groupId>
+      <groupId>org.apache.commons</groupId>
-      <artifactId>commons-lang</artifactId>
+      <artifactId>commons-lang3</artifactId>
     </dependency>
 
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-email</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.freemarker</groupId>
       <artifactId>freemarker</artifactId>
     </dependency>
 
     <dependency>
-      <groupId>org.glassfish</groupId>
+      <groupId>jakarta.json</groupId>
-      <artifactId>javax.json</artifactId>
+      <artifactId>jakarta.json-api</artifactId>
     </dependency>
 
     <dependency>
@@ -76,17 +66,17 @@
       <groupId>log4j</groupId>
       <artifactId>log4j</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-log4j12</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-api</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>jcl-over-slf4j</artifactId>
@@ -96,17 +86,17 @@
       <groupId>at.favre.lib</groupId>
       <artifactId>bcrypt</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.apache.lucene</groupId>
       <artifactId>lucene-core</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.apache.lucene</groupId>
       <artifactId>lucene-analyzers-common</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.apache.lucene</groupId>
       <artifactId>lucene-queryparser</artifactId>
@@ -122,11 +112,6 @@
       <artifactId>lucene-highlighter</artifactId>
     </dependency>
 
-    <dependency>
-      <groupId>com.sun.mail</groupId>
-      <artifactId>javax.mail</artifactId>
-    </dependency>
-
     <dependency>
       <groupId>com.squareup.okhttp3</groupId>
       <artifactId>okhttp</artifactId>
@@ -134,7 +119,12 @@
 
     <dependency>
       <groupId>org.apache.directory.api</groupId>
-      <artifactId>api-all</artifactId>
+      <artifactId>api-ldap-client-api</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>org.apache.directory.api</groupId>
+      <artifactId>api-ldap-codec-standalone</artifactId>
     </dependency>
 
     <!-- Only there to read old index and rebuild them -->
@@ -142,22 +132,22 @@
       <groupId>org.apache.lucene</groupId>
       <artifactId>lucene-backward-codecs</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.imgscalr</groupId>
       <artifactId>imgscalr-lib</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.apache.pdfbox</groupId>
       <artifactId>pdfbox</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.bouncycastle</groupId>
       <artifactId>bcprov-jdk15on</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>fr.opensagres.xdocreport</groupId>
       <artifactId>fr.opensagres.odfdom.converter.pdf</artifactId>
@@ -195,39 +185,20 @@
       <artifactId>postgresql</artifactId>
     </dependency>
 
-    <!-- JDK 11 JAXB dependencies -->
-    <dependency>
-      <groupId>javax.xml.bind</groupId>
-      <artifactId>jaxb-api</artifactId>
-      <version>2.3.0</version>
-    </dependency>
-
-    <dependency>
-      <groupId>com.sun.xml.bind</groupId>
-      <artifactId>jaxb-core</artifactId>
-      <version>2.3.0</version>
-    </dependency>
-
-    <dependency>
-      <groupId>com.sun.xml.bind</groupId>
-      <artifactId>jaxb-impl</artifactId>
-      <version>2.3.0</version>
-    </dependency>
-
     <!-- Test dependencies -->
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
       <scope>test</scope>
     </dependency>
-    
+
     <dependency>
       <groupId>com.h2database</groupId>
       <artifactId>h2</artifactId>
       <scope>test</scope>
     </dependency>
   </dependencies>
-  
+
   <profiles>
     <!-- Development profile (active by default) -->
     <profile>
@@ -239,7 +210,7 @@
           <value>dev</value>
         </property>
       </activation>
-      
+
       <build>
         <resources>
           <resource>
@@ -255,7 +226,7 @@
       <id>prod</id>
     </profile>
   </profiles>
-  
+
   <build>
     <resources>
       <resource>

docs-core/src/main/java/com/sismics/docs/core/constant/ConfigType.java

@@ -1,9 +1,9 @@
 package com.sismics.docs.core.constant;
 
 /**
- * Configuration parameters. 
+ * Configuration parameters.
  *
- * @author jtremeaux 
+ * @author jtremeaux
  */
 public enum ConfigType {
     /**
@@ -20,6 +20,11 @@ public enum ConfigType {
      */
     GUEST_LOGIN,
 
+    /**
+     * OCR enabled.
+     */
+    OCR_ENABLED,
+
     /**
      * Default language.
      */
@@ -40,6 +45,7 @@ public enum ConfigType {
     INBOX_ENABLED,
     INBOX_HOSTNAME,
     INBOX_PORT,
+    INBOX_STARTTLS,
     INBOX_USERNAME,
     INBOX_PASSWORD,
     INBOX_FOLDER,
@@ -53,6 +59,7 @@ public enum ConfigType {
     LDAP_ENABLED,
     LDAP_HOST,
     LDAP_PORT,
+    LDAP_USESSL,
     LDAP_ADMIN_DN,
     LDAP_ADMIN_PASSWORD,
     LDAP_BASE_DN,

docs-core/src/main/java/com/sismics/docs/core/constant/Constants.java

@@ -43,7 +43,7 @@ public class Constants {
     /**
      * Supported document languages.
      */
-    public static final List<String> SUPPORTED_LANGUAGES = Lists.newArrayList("eng", "fra", "ita", "deu", "spa", "por", "pol", "rus", "ukr", "ara", "hin", "chi_sim", "chi_tra", "jpn", "tha", "kor", "nld", "tur", "heb", "hun", "fin", "swe", "lav", "dan", "nor", "vie");
+    public static final List<String> SUPPORTED_LANGUAGES = Lists.newArrayList("eng", "fra", "ita", "deu", "spa", "por", "pol", "rus", "ukr", "ara", "hin", "chi_sim", "chi_tra", "jpn", "tha", "kor", "nld", "tur", "heb", "hun", "fin", "swe", "lav", "dan", "nor", "vie", "ces", "sqi");
 
     /**
      * Base URL environment variable.

docs-core/src/main/java/com/sismics/docs/core/dao/AclDao.java

@@ -10,8 +10,8 @@ import com.sismics.docs.core.util.AuditLogUtil;
 import com.sismics.docs.core.util.SecurityUtil;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;

docs-core/src/main/java/com/sismics/docs/core/dao/AuditLogDao.java

@@ -12,7 +12,7 @@ import com.sismics.docs.core.util.jpa.QueryParam;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.sql.Timestamp;
 import java.util.*;
 

docs-core/src/main/java/com/sismics/docs/core/dao/AuthenticationTokenDao.java

@@ -4,8 +4,8 @@ import com.sismics.docs.core.model.jpa.AuthenticationToken;
 import com.sismics.util.context.ThreadLocalContext;
 import org.joda.time.DateTime;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.Date;
 import java.util.List;
 import java.util.UUID;

docs-core/src/main/java/com/sismics/docs/core/dao/CommentDao.java

@@ -6,9 +6,9 @@ import com.sismics.docs.core.model.jpa.Comment;
 import com.sismics.docs.core.util.AuditLogUtil;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.sql.Timestamp;
 import java.util.ArrayList;
 import java.util.Date;

docs-core/src/main/java/com/sismics/docs/core/dao/ConfigDao.java

@@ -4,8 +4,8 @@ import com.sismics.docs.core.constant.ConfigType;
 import com.sismics.docs.core.model.jpa.Config;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
 
 /**
  * Configuration parameter DAO.

docs-core/src/main/java/com/sismics/docs/core/dao/ContributorDao.java

@@ -4,8 +4,8 @@ import com.sismics.docs.core.dao.dto.ContributorDto;
 import com.sismics.docs.core.model.jpa.Contributor;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;

docs-core/src/main/java/com/sismics/docs/core/dao/DocumentDao.java

@@ -7,9 +7,10 @@ import com.sismics.docs.core.model.jpa.Document;
 import com.sismics.docs.core.util.AuditLogUtil;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
 import java.sql.Timestamp;
 import java.util.Date;
 import java.util.List;
@@ -50,10 +51,9 @@ public class DocumentDao {
      * @param limit Limit
      * @return List of documents
      */
-    @SuppressWarnings("unchecked")
     public List<Document> findAll(int offset, int limit) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select d from Document d where d.deleteDate is null");
+        TypedQuery<Document> q = em.createQuery("select d from Document d where d.deleteDate is null", Document.class);
         q.setFirstResult(offset);
         q.setMaxResults(limit);
         return q.getResultList();
@@ -65,10 +65,9 @@ public class DocumentDao {
      * @param userId User ID
      * @return List of documents
      */
-    @SuppressWarnings("unchecked")
     public List<Document> findByUserId(String userId) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select d from Document d where d.userId = :userId and d.deleteDate is null");
+        TypedQuery<Document> q = em.createQuery("select d from Document d where d.userId = :userId and d.deleteDate is null", Document.class);
         q.setParameter("userId", userId);
         return q.getResultList();
     }
@@ -88,7 +87,7 @@ public class DocumentDao {
         }
 
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        StringBuilder sb = new StringBuilder("select distinct d.DOC_ID_C, d.DOC_TITLE_C, d.DOC_DESCRIPTION_C, d.DOC_SUBJECT_C, d.DOC_IDENTIFIER_C, d.DOC_PUBLISHER_C, d.DOC_FORMAT_C, d.DOC_SOURCE_C, d.DOC_TYPE_C, d.DOC_COVERAGE_C, d.DOC_RIGHTS_C, d.DOC_CREATEDATE_D, d.DOC_UPDATEDATE_D, d.DOC_LANGUAGE_C, ");
+        StringBuilder sb = new StringBuilder("select distinct d.DOC_ID_C, d.DOC_TITLE_C, d.DOC_DESCRIPTION_C, d.DOC_SUBJECT_C, d.DOC_IDENTIFIER_C, d.DOC_PUBLISHER_C, d.DOC_FORMAT_C, d.DOC_SOURCE_C, d.DOC_TYPE_C, d.DOC_COVERAGE_C, d.DOC_RIGHTS_C, d.DOC_CREATEDATE_D, d.DOC_UPDATEDATE_D, d.DOC_LANGUAGE_C, d.DOC_IDFILE_C,");
         sb.append(" (select count(s.SHA_ID_C) from T_SHARE s, T_ACL ac where ac.ACL_SOURCEID_C = d.DOC_ID_C and ac.ACL_TARGETID_C = s.SHA_ID_C and ac.ACL_DELETEDATE_D is null and s.SHA_DELETEDATE_D is null) shareCount, ");
         sb.append(" (select count(f.FIL_ID_C) from T_FILE f where f.FIL_DELETEDATE_D is null and f.FIL_IDDOC_C = d.DOC_ID_C) fileCount, ");
         sb.append(" u.USE_USERNAME_C ");
@@ -122,6 +121,7 @@ public class DocumentDao {
         documentDto.setCreateTimestamp(((Timestamp) o[i++]).getTime());
         documentDto.setUpdateTimestamp(((Timestamp) o[i++]).getTime());
         documentDto.setLanguage((String) o[i++]);
+        documentDto.setFileId((String) o[i++]);
         documentDto.setShared(((Number) o[i++]).intValue() > 0);
         documentDto.setFileCount(((Number) o[i++]).intValue());
         documentDto.setCreator((String) o[i]);
@@ -138,16 +138,16 @@ public class DocumentDao {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
             
         // Get the document
-        Query q = em.createQuery("select d from Document d where d.id = :id and d.deleteDate is null");
+        TypedQuery<Document> dq = em.createQuery("select d from Document d where d.id = :id and d.deleteDate is null", Document.class);
-        q.setParameter("id", id);
+        dq.setParameter("id", id);
-        Document documentDb = (Document) q.getSingleResult();
+        Document documentDb = dq.getSingleResult();
         
         // Delete the document
         Date dateNow = new Date();
         documentDb.setDeleteDate(dateNow);
 
         // Delete linked data
-        q = em.createQuery("update File f set f.deleteDate = :dateNow where f.documentId = :documentId and f.deleteDate is null");
+        Query q = em.createQuery("update File f set f.deleteDate = :dateNow where f.documentId = :documentId and f.deleteDate is null");
         q.setParameter("documentId", id);
         q.setParameter("dateNow", dateNow);
         q.executeUpdate();
@@ -179,10 +179,10 @@ public class DocumentDao {
      */
     public Document getById(String id) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select d from Document d where d.id = :id and d.deleteDate is null");
+        TypedQuery<Document> q = em.createQuery("select d from Document d where d.id = :id and d.deleteDate is null", Document.class);
         q.setParameter("id", id);
         try {
-            return (Document) q.getSingleResult();
+            return q.getSingleResult();
         } catch (NoResultException e) {
             return null;
         }
@@ -199,9 +199,9 @@ public class DocumentDao {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
 
         // Get the document
-        Query q = em.createQuery("select d from Document d where d.id = :id and d.deleteDate is null");
+        TypedQuery<Document> q = em.createQuery("select d from Document d where d.id = :id and d.deleteDate is null", Document.class);
         q.setParameter("id", document.getId());
-        Document documentDb = (Document) q.getSingleResult();
+        Document documentDb = q.getSingleResult();
 
         // Update the document
         documentDb.setTitle(document.getTitle());
@@ -237,7 +237,6 @@ public class DocumentDao {
         query.setParameter("fileId", document.getFileId());
         query.setParameter("id", document.getId());
         query.executeUpdate();
-
     }
 
     /**

docs-core/src/main/java/com/sismics/docs/core/dao/DocumentMetadataDao.java

@@ -5,8 +5,8 @@ import com.sismics.docs.core.dao.dto.DocumentMetadataDto;
 import com.sismics.docs.core.model.jpa.DocumentMetadata;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;

docs-core/src/main/java/com/sismics/docs/core/dao/FileDao.java

@@ -4,12 +4,16 @@ import com.sismics.docs.core.constant.AuditLogType;
 import com.sismics.docs.core.model.jpa.File;
 import com.sismics.docs.core.util.AuditLogUtil;
 import com.sismics.util.context.ThreadLocalContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
 
-import javax.persistence.EntityManager;
+import java.util.Collections;
-import javax.persistence.NoResultException;
-import javax.persistence.Query;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.UUID;
 
 /**
@@ -47,10 +51,9 @@ public class FileDao {
      * @param limit Limit
      * @return List of files
      */
-    @SuppressWarnings("unchecked")
     public List<File> findAll(int offset, int limit) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select f from File f where f.deleteDate is null");
+        TypedQuery<File> q = em.createQuery("select f from File f where f.deleteDate is null", File.class);
         q.setFirstResult(offset);
         q.setMaxResults(limit);
         return q.getResultList();
@@ -62,28 +65,38 @@ public class FileDao {
      * @param userId User ID
      * @return List of files
      */
-    @SuppressWarnings("unchecked")
     public List<File> findByUserId(String userId) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select f from File f where f.userId = :userId and f.deleteDate is null");
+        TypedQuery<File> q = em.createQuery("select f from File f where f.userId = :userId and f.deleteDate is null", File.class);
         q.setParameter("userId", userId);
         return q.getResultList();
     }
+
+    /**
+     * Returns a list of active files.
+     *
+     * @param ids Files IDs
+     * @return List of files
+     */
+    public List<File> getFiles(List<String> ids) {
+        EntityManager em = ThreadLocalContext.get().getEntityManager();
+        TypedQuery<File> q = em.createQuery("select f from File f where f.id in :ids and f.deleteDate is null", File.class);
+        q.setParameter("ids", ids);
+        return q.getResultList();
+    }
     
     /**
-     * Returns an active file.
+     * Returns an active file or null.
      * 
      * @param id File ID
-     * @return Document
+     * @return File
      */
     public File getFile(String id) {
-        EntityManager em = ThreadLocalContext.get().getEntityManager();
+        List<File> files = getFiles(List.of(id));
-        Query q = em.createQuery("select f from File f where f.id = :id and f.deleteDate is null");
+        if (files.isEmpty()) {
-        q.setParameter("id", id);
-        try {
-            return (File) q.getSingleResult();
-        } catch (NoResultException e) {
             return null;
+        } else {
+            return files.get(0);
         }
     }
     
@@ -92,15 +105,15 @@ public class FileDao {
      * 
      * @param id File ID
      * @param userId User ID
-     * @return Document
+     * @return File
      */
     public File getFile(String id, String userId) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select f from File f where f.id = :id and f.userId = :userId and f.deleteDate is null");
+        TypedQuery<File> q = em.createQuery("select f from File f where f.id = :id and f.userId = :userId and f.deleteDate is null", File.class);
         q.setParameter("id", id);
         q.setParameter("userId", userId);
         try {
-            return (File) q.getSingleResult();
+            return q.getSingleResult();
         } catch (NoResultException e) {
             return null;
         }
@@ -116,9 +129,9 @@ public class FileDao {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
             
         // Get the file
-        Query q = em.createQuery("select f from File f where f.id = :id and f.deleteDate is null");
+        TypedQuery<File> q = em.createQuery("select f from File f where f.id = :id and f.deleteDate is null", File.class);
         q.setParameter("id", id);
-        File fileDb = (File) q.getSingleResult();
+        File fileDb = q.getSingleResult();
         
         // Delete the file
         Date dateNow = new Date();
@@ -138,9 +151,9 @@ public class FileDao {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
         
         // Get the file
-        Query q = em.createQuery("select f from File f where f.id = :id and f.deleteDate is null");
+        TypedQuery<File> q = em.createQuery("select f from File f where f.id = :id and f.deleteDate is null", File.class);
         q.setParameter("id", file.getId());
-        File fileDb = (File) q.getSingleResult();
+        File fileDb = q.getSingleResult();
 
         // Update the file
         fileDb.setDocumentId(file.getDocumentId());
@@ -150,6 +163,7 @@ public class FileDao {
         fileDb.setMimeType(file.getMimeType());
         fileDb.setVersionId(file.getVersionId());
         fileDb.setLatestVersion(file.isLatestVersion());
+        fileDb.setSize(file.getSize());
 
         return file;
     }
@@ -162,46 +176,82 @@ public class FileDao {
      */
     public File getActiveById(String id) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select f from File f where f.id = :id and f.deleteDate is null");
+        TypedQuery<File> q = em.createQuery("select f from File f where f.id = :id and f.deleteDate is null", File.class);
         q.setParameter("id", id);
         try {
-            return (File) q.getSingleResult();
+            return q.getSingleResult();
         } catch (NoResultException e) {
             return null;
         }
     }
     
     /**
-     * Get files by document ID or all orphan files of an user.
+     * Get files by document ID or all orphan files of a user.
      * 
      * @param userId User ID
      * @param documentId Document ID
      * @return List of files
      */
-    @SuppressWarnings("unchecked")
     public List<File> getByDocumentId(String userId, String documentId) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
         if (documentId == null) {
-            Query q = em.createQuery("select f from File f where f.documentId is null and f.deleteDate is null and f.latestVersion = true and f.userId = :userId order by f.createDate asc");
+            TypedQuery<File> q = em.createQuery("select f from File f where f.documentId is null and f.deleteDate is null and f.latestVersion = true and f.userId = :userId order by f.createDate asc", File.class);
             q.setParameter("userId", userId);
             return q.getResultList();
+        } else {
+            return getByDocumentsIds(Collections.singleton(documentId));
         }
-        Query q = em.createQuery("select f from File f where f.documentId = :documentId and f.latestVersion = true and f.deleteDate is null order by f.order asc");
+    }
-        q.setParameter("documentId", documentId);
+
+    /**
+     * Get files by documents IDs.
+     *
+     * @param documentIds Documents IDs
+     * @return List of files
+     */
+    public List<File> getByDocumentsIds(Iterable<String> documentIds) {
+        EntityManager em = ThreadLocalContext.get().getEntityManager();
+        TypedQuery<File> q = em.createQuery("select f from File f where f.documentId in :documentIds and f.latestVersion = true and f.deleteDate is null order by f.order asc", File.class);
+        q.setParameter("documentIds", documentIds);
         return q.getResultList();
     }
 
+    /**
+     * Get files count by documents IDs.
+     *
+     * @param documentIds Documents IDs
+     * @return the number of files per document id
+     */
+    public Map<String, Long> countByDocumentsIds(Iterable<String> documentIds) {
+        EntityManager em = ThreadLocalContext.get().getEntityManager();
+        Query q = em.createQuery("select f.documentId, count(*) from File f where f.documentId in :documentIds and f.latestVersion = true and f.deleteDate is null group by (f.documentId)");
+        q.setParameter("documentIds", documentIds);
+        Map<String, Long> result = new HashMap<>();
+        q.getResultList().forEach(o -> {
+            Object[] resultLine = (Object[]) o;
+            result.put((String) resultLine[0], (Long) resultLine[1]);
+        });
+        return result;
+    }
+
     /**
      * Get all files from a version.
      *
      * @param versionId Version ID
      * @return List of files
      */
-    @SuppressWarnings("unchecked")
     public List<File> getByVersionId(String versionId) {
         EntityManager em = ThreadLocalContext.get().getEntityManager();
-        Query q = em.createQuery("select f from File f where f.versionId = :versionId and f.deleteDate is null order by f.order asc");
+        TypedQuery<File> q = em.createQuery("select f from File f where f.versionId = :versionId and f.deleteDate is null order by f.order asc", File.class);
         q.setParameter("versionId", versionId);
         return q.getResultList();
     }
+
+    public List<File> getFilesWithUnknownSize(int limit) {
+        EntityManager em = ThreadLocalContext.get().getEntityManager();
+        TypedQuery<File> q = em.createQuery("select f from File f where f.size = :size and f.deleteDate is null order by f.order asc", File.class);
+        q.setParameter("size", File.UNKNOWN_SIZE);
+        q.setMaxResults(limit);
+        return q.getResultList();
+    }
 }

docs-core/src/main/java/com/sismics/docs/core/dao/GroupDao.java

@@ -12,9 +12,9 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.*;
 
 /**
@@ -183,12 +183,10 @@ public class GroupDao {
         }
         
         criteriaList.add("g.GRP_DELETEDATE_D is null");
-        
+
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
+
-        }
-        
         // Perform the search
         QueryParam queryParam = QueryUtil.getSortedQueryParam(new QueryParam(sb.toString(), parameterMap), sortCriteria);
         @SuppressWarnings("unchecked")

docs-core/src/main/java/com/sismics/docs/core/dao/MetadataDao.java

@@ -12,9 +12,9 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.*;
 
 /**
@@ -123,10 +123,8 @@ public class MetadataDao {
 
         criteriaList.add("m.MET_DELETEDATE_D is null");
 
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
-        }
 
         // Perform the search
         QueryParam queryParam = QueryUtil.getSortedQueryParam(new QueryParam(sb.toString(), parameterMap), sortCriteria);

docs-core/src/main/java/com/sismics/docs/core/dao/PasswordRecoveryDao.java

@@ -6,9 +6,9 @@ import com.sismics.util.context.ThreadLocalContext;
 import org.joda.time.DateTime;
 import org.joda.time.DurationFieldType;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.Date;
 import java.util.UUID;
 

docs-core/src/main/java/com/sismics/docs/core/dao/RelationDao.java

@@ -4,8 +4,8 @@ import com.sismics.docs.core.dao.dto.RelationDto;
 import com.sismics.docs.core.model.jpa.Relation;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.*;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/dao/RoleBaseFunctionDao.java

@@ -3,8 +3,8 @@ package com.sismics.docs.core.dao;
 import com.google.common.collect.Sets;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.Set;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/dao/RouteDao.java

@@ -11,7 +11,7 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.sql.Timestamp;
 import java.util.*;
 
@@ -64,10 +64,8 @@ public class RouteDao {
         }
         criteriaList.add("r.RTE_DELETEDATE_D is null");
 
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
-        }
 
         // Perform the search
         QueryParam queryParam = QueryUtil.getSortedQueryParam(new QueryParam(sb.toString(), parameterMap), sortCriteria);

docs-core/src/main/java/com/sismics/docs/core/dao/RouteModelDao.java

@@ -12,9 +12,9 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.sql.Timestamp;
 import java.util.*;
 
@@ -145,10 +145,8 @@ public class RouteModelDao {
 
         criteriaList.add("rm.RTM_DELETEDATE_D is null");
 
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
-        }
 
         // Perform the search
         QueryParam queryParam = QueryUtil.getSortedQueryParam(new QueryParam(sb.toString(), parameterMap), sortCriteria);

docs-core/src/main/java/com/sismics/docs/core/dao/RouteStepDao.java

@@ -12,8 +12,8 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.sql.Timestamp;
 import java.util.*;
 
@@ -90,10 +90,8 @@ public class RouteStepDao {
         }
         criteriaList.add("rs.RTP_DELETEDATE_D is null");
 
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
-        }
 
         // Perform the search
         QueryParam queryParam = QueryUtil.getSortedQueryParam(new QueryParam(sb.toString(), parameterMap), sortCriteria);

docs-core/src/main/java/com/sismics/docs/core/dao/ShareDao.java

@@ -3,8 +3,8 @@ package com.sismics.docs.core.dao;
 import com.sismics.docs.core.model.jpa.Share;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.Date;
 import java.util.UUID;
 
@@ -19,7 +19,6 @@ public class ShareDao {
      * 
      * @param share Share
      * @return New ID
-     * @throws Exception
      */
     public String create(Share share) {
         // Create the UUID

docs-core/src/main/java/com/sismics/docs/core/dao/TagDao.java

@@ -13,9 +13,9 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.*;
 
 /**
@@ -199,10 +199,8 @@ public class TagDao {
 
         criteriaList.add("t.TAG_DELETEDATE_D is null");
 
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
-        }
 
         // Perform the search
         QueryParam queryParam = QueryUtil.getSortedQueryParam(new QueryParam(sb.toString(), parameterMap), sortCriteria);

docs-core/src/main/java/com/sismics/docs/core/dao/UserDao.java

@@ -1,6 +1,7 @@
 package com.sismics.docs.core.dao;
 
 import com.google.common.base.Joiner;
+import com.google.common.base.Strings;
 import at.favre.lib.crypto.bcrypt.BCrypt;
 import org.joda.time.DateTime;
 import org.slf4j.Logger;
@@ -18,9 +19,9 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.sql.Timestamp;
 import java.util.*;
 
@@ -289,7 +290,7 @@ public class UserDao {
     private String hashPassword(String password) {
         int bcryptWork = Constants.DEFAULT_BCRYPT_WORK;
         String envBcryptWork = System.getenv(Constants.BCRYPT_WORK_ENV);
-        if (envBcryptWork != null) {
+        if (!Strings.isNullOrEmpty(envBcryptWork)) {
             try {
                 int envBcryptWorkInt = Integer.parseInt(envBcryptWork);
                 if (envBcryptWorkInt >= 4 && envBcryptWorkInt <= 31) {

docs-core/src/main/java/com/sismics/docs/core/dao/VocabularyDao.java

@@ -3,9 +3,9 @@ package com.sismics.docs.core.dao;
 import com.sismics.docs.core.model.jpa.Vocabulary;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.List;
 import java.util.UUID;
 
@@ -20,7 +20,6 @@ public class VocabularyDao {
      * 
      * @param vocabulary Vocabulary
      * @return New ID
-     * @throws Exception
      */
     public String create(Vocabulary vocabulary) {
         // Create the UUID

docs-core/src/main/java/com/sismics/docs/core/dao/WebhookDao.java

@@ -9,9 +9,9 @@ import com.sismics.docs.core.util.jpa.QueryUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.sql.Timestamp;
 import java.util.*;
 
@@ -42,11 +42,9 @@ public class WebhookDao {
         }
         criteriaList.add("w.WHK_DELETEDATE_D is null");
 
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
+
-        }
-        
         // Perform the search
         QueryParam queryParam = QueryUtil.getSortedQueryParam(new QueryParam(sb.toString(), parameterMap), sortCriteria);
         @SuppressWarnings("unchecked")

docs-core/src/main/java/com/sismics/docs/core/dao/criteria/DocumentCriteria.java

@@ -1,5 +1,6 @@
 package com.sismics.docs.core.dao.criteria;
 
+import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 
@@ -18,7 +19,7 @@ public class DocumentCriteria {
     /**
      * Search query.
      */
-    private String search;
+    private String simpleSearch;
     
     /**
      * Full content search query.
@@ -49,13 +50,13 @@ public class DocumentCriteria {
      * Tag IDs.
      * The first level list will be AND'ed and the second level list will be OR'ed.
      */
-    private List<List<String>> tagIdList;
+    private List<List<String>> tagIdList = new ArrayList<>();
     
     /**
      * Tag IDs to exclude.
      * The first and second level list will be excluded.
      */
-    private List<List<String>> excludedTagIdList;
+    private List<List<String>> excludedTagIdList = new ArrayList<>();
 
     /**
      * Shared status.
@@ -83,9 +84,9 @@ public class DocumentCriteria {
     private String mimeType;
 
     /**
-     * The title.
+     * Titles to include.
      */
-    private String title;
+    private List<String> titleList = new ArrayList<>();
 
     public List<String> getTargetIdList() {
         return targetIdList;
@@ -95,12 +96,12 @@ public class DocumentCriteria {
         this.targetIdList = targetIdList;
     }
 
-    public String getSearch() {
+    public String getSimpleSearch() {
-        return search;
+        return simpleSearch;
     }
 
-    public void setSearch(String search) {
+    public void setSimpleSearch(String search) {
-        this.search = search;
+        this.simpleSearch = search;
     }
 
     public String getFullSearch() {
@@ -131,19 +132,10 @@ public class DocumentCriteria {
         return tagIdList;
     }
 
-    public void setTagIdList(List<List<String>> tagIdList) {
-        this.tagIdList = tagIdList;
-    }
-
     public List<List<String>> getExcludedTagIdList() {
         return excludedTagIdList;
     }
 
-    public DocumentCriteria setExcludedTagIdList(List<List<String>> excludedTagIdList) {
-        this.excludedTagIdList = excludedTagIdList;
-        return this;
-    }
-
     public Boolean getShared() {
         return shared;
     }
@@ -167,11 +159,7 @@ public class DocumentCriteria {
     public void setCreatorId(String creatorId) {
         this.creatorId = creatorId;
     }
-
+ 
-    public Boolean getActiveRoute() {
-        return activeRoute;
-    }
-
     public Date getUpdateDateMin() {
         return updateDateMin;
     }
@@ -188,6 +176,10 @@ public class DocumentCriteria {
         this.updateDateMax = updateDateMax;
     }
 
+    public Boolean getActiveRoute() {
+        return activeRoute;
+    }
+
     public void setActiveRoute(Boolean activeRoute) {
         this.activeRoute = activeRoute;
     }
@@ -200,11 +192,7 @@ public class DocumentCriteria {
         this.mimeType = mimeType;
     }
 
-    public String getTitle() {
+    public List<String> getTitleList() {
-        return title;
+        return titleList;
-    }
-
-    public void setTitle(String title) {
-        this.title = title;
     }
 }

docs-core/src/main/java/com/sismics/docs/core/dao/dto/RouteStepDto.java

@@ -3,8 +3,8 @@ package com.sismics.docs.core.dao.dto;
 import com.sismics.docs.core.constant.RouteStepType;
 import com.sismics.util.JsonUtil;
 
-import javax.json.Json;
+import jakarta.json.Json;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.JsonObjectBuilder;
 
 /**
  * Route step DTO.

docs-core/src/main/java/com/sismics/docs/core/event/FileDeletedAsyncEvent.java

@@ -13,6 +13,8 @@ public class FileDeletedAsyncEvent extends UserEvent {
      */
     private String fileId;
 
+    private Long fileSize;
+
     public String getFileId() {
         return fileId;
     }
@@ -21,10 +23,19 @@ public class FileDeletedAsyncEvent extends UserEvent {
         this.fileId = fileId;
     }
 
+    public Long getFileSize() {
+        return fileSize;
+    }
+
+    public void setFileSize(Long fileSize) {
+        this.fileSize = fileSize;
+    }
+
     @Override
     public String toString() {
         return MoreObjects.toStringHelper(this)
             .add("fileId", fileId)
+            .add("fileSize", fileSize)
             .toString();
     }
-}
+}

docs-core/src/main/java/com/sismics/docs/core/listener/async/FileDeletedAsyncListener.java

@@ -2,8 +2,11 @@ package com.sismics.docs.core.listener.async;
 
 import com.google.common.eventbus.AllowConcurrentEvents;
 import com.google.common.eventbus.Subscribe;
+import com.sismics.docs.core.dao.UserDao;
 import com.sismics.docs.core.event.FileDeletedAsyncEvent;
 import com.sismics.docs.core.model.context.AppContext;
+import com.sismics.docs.core.model.jpa.File;
+import com.sismics.docs.core.model.jpa.User;
 import com.sismics.docs.core.util.FileUtil;
 import com.sismics.docs.core.util.TransactionUtil;
 import org.slf4j.Logger;
@@ -11,7 +14,7 @@ import org.slf4j.LoggerFactory;
 
 /**
  * Listener on file deleted.
- * 
+ *
  * @author bgamard
  */
 public class FileDeletedAsyncListener {
@@ -22,7 +25,7 @@ public class FileDeletedAsyncListener {
 
     /**
      * File deleted.
-     * 
+     *
      * @param event File deleted event
      * @throws Exception e
      */
@@ -32,6 +35,24 @@ public class FileDeletedAsyncListener {
         if (log.isInfoEnabled()) {
             log.info("File deleted event: " + event.toString());
         }
+        TransactionUtil.handle(() -> {
+            // Update the user quota
+            UserDao userDao = new UserDao();
+            User user = userDao.getById(event.getUserId());
+            if (user != null) {
+                Long fileSize = event.getFileSize();
+
+                if (fileSize.equals(File.UNKNOWN_SIZE)) {
+                    // The file size was not in the database, in this case we need to get from the unencrypted size.
+                    fileSize = FileUtil.getFileSize(event.getFileId(), user);
+                }
+
+                if (! fileSize.equals(File.UNKNOWN_SIZE)) {
+                    user.setStorageCurrent(user.getStorageCurrent() - fileSize);
+                    userDao.updateQuota(user);
+                }
+            }
+        });
 
         // Delete the file from storage
         FileUtil.delete(event.getFileId());

docs-core/src/main/java/com/sismics/docs/core/model/context/AppContext.java

@@ -1,5 +1,6 @@
 package com.sismics.docs.core.model.context;
 
+import com.google.common.base.Strings;
 import com.google.common.collect.Lists;
 import com.google.common.eventbus.AsyncEventBus;
 import com.google.common.eventbus.EventBus;
@@ -8,6 +9,7 @@ import com.sismics.docs.core.dao.UserDao;
 import com.sismics.docs.core.listener.async.*;
 import com.sismics.docs.core.model.jpa.User;
 import com.sismics.docs.core.service.FileService;
+import com.sismics.docs.core.service.FileSizeService;
 import com.sismics.docs.core.service.InboxService;
 import com.sismics.docs.core.util.PdfUtil;
 import com.sismics.docs.core.util.indexing.IndexingHandler;
@@ -64,6 +66,11 @@ public class AppContext {
      */
     private FileService fileService;
 
+    /**
+     * File size service.
+     */
+    private FileSizeService fileSizeService;
+
     /**
      * Asynchronous executors.
      */
@@ -101,12 +108,17 @@ public class AppContext {
         inboxService.startAsync();
         inboxService.awaitRunning();
 
+        // Start file size service
+        fileSizeService = new FileSizeService();
+        fileSizeService.startAsync();
+        fileSizeService.awaitRunning();
+
         // Register fonts
         PdfUtil.registerFonts();
 
         // Change the admin password if needed
         String envAdminPassword = System.getenv(Constants.ADMIN_PASSWORD_INIT_ENV);
-        if (envAdminPassword != null) {
+        if (!Strings.isNullOrEmpty(envAdminPassword)) {
             UserDao userDao = new UserDao();
             User adminUser = userDao.getById("admin");
             if (Constants.DEFAULT_ADMIN_PASSWORD.equals(adminUser.getPassword())) {
@@ -117,7 +129,7 @@ public class AppContext {
 
         // Change the admin email if needed
         String envAdminEmail = System.getenv(Constants.ADMIN_EMAIL_INIT_ENV);
-        if (envAdminEmail != null) {
+        if (!Strings.isNullOrEmpty(envAdminEmail)) {
             UserDao userDao = new UserDao();
             User adminUser = userDao.getById("admin");
             if (Constants.DEFAULT_ADMIN_EMAIL.equals(adminUser.getEmail())) {
@@ -237,6 +249,10 @@ public class AppContext {
             fileService.stopAsync();
         }
 
+        if (fileSizeService != null) {
+            fileSizeService.stopAsync();
+        }
+
         instance = null;
     }
 }

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Acl.java

@@ -4,7 +4,7 @@ import com.google.common.base.MoreObjects;
 import com.sismics.docs.core.constant.AclType;
 import com.sismics.docs.core.constant.PermType;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/AuditLog.java

@@ -2,12 +2,12 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.EnumType;
+import jakarta.persistence.EnumType;
-import javax.persistence.Enumerated;
+import jakarta.persistence.Enumerated;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 import com.sismics.docs.core.constant.AuditLogType;

docs-core/src/main/java/com/sismics/docs/core/model/jpa/AuthenticationToken.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/BaseFunction.java

@@ -1,9 +1,9 @@
 package com.sismics.docs.core.model.jpa;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Comment.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Config.java

@@ -1,11 +1,11 @@
 package com.sismics.docs.core.model.jpa;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.EnumType;
+import jakarta.persistence.EnumType;
-import javax.persistence.Enumerated;
+import jakarta.persistence.Enumerated;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 import com.sismics.docs.core.constant.ConfigType;

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Contributor.java

@@ -1,9 +1,9 @@
 package com.sismics.docs.core.model.jpa;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Document.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import com.google.common.base.MoreObjects;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/DocumentMetadata.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import com.google.common.base.MoreObjects;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 import java.io.Serializable;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/DocumentTag.java

@@ -3,10 +3,10 @@ package com.sismics.docs.core.model.jpa;
 import java.io.Serializable;
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/File.java

@@ -4,7 +4,7 @@ import com.google.common.base.MoreObjects;
 import com.google.common.base.Strings;
 import com.sismics.util.mime.MimeTypeUtil;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Date;
 
 /**
@@ -88,6 +88,14 @@ public class File implements Loggable {
     @Column(name = "FIL_LATESTVERSION_B", nullable = false)
     private boolean latestVersion;
 
+    public static final Long UNKNOWN_SIZE = -1L;
+
+    /**
+     * Can be {@link File#UNKNOWN_SIZE} if the size has not been stored in the database when the file has been uploaded
+     */
+    @Column(name = "FIL_SIZE_N", nullable = false)
+    private Long size;
+
     /**
      * Private key to decrypt the file.
      * Not saved to database, of course.
@@ -204,6 +212,18 @@ public class File implements Loggable {
         return this;
     }
 
+    /**
+     * Can return {@link File#UNKNOWN_SIZE} if the file size is not stored in the database.
+     */
+    public Long getSize() {
+        return size;
+    }
+
+    public File setSize(Long size) {
+        this.size = size;
+        return this;
+    }
+
     @Override
     public String toString() {
         return MoreObjects.toStringHelper(this)

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Group.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Metadata.java

@@ -3,7 +3,7 @@ package com.sismics.docs.core.model.jpa;
 import com.google.common.base.MoreObjects;
 import com.sismics.docs.core.constant.MetadataType;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/PasswordRecovery.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import com.google.common.base.MoreObjects;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Relation.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Role.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/RoleBaseFunction.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Route.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import com.google.common.base.MoreObjects;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/RouteModel.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import com.google.common.base.MoreObjects;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/RouteStep.java

@@ -4,7 +4,7 @@ import com.google.common.base.MoreObjects;
 import com.sismics.docs.core.constant.RouteStepTransition;
 import com.sismics.docs.core.constant.RouteStepType;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Share.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Tag.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/User.java

@@ -2,10 +2,10 @@ package com.sismics.docs.core.model.jpa;
 
 import com.google.common.base.MoreObjects;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/model/jpa/UserGroup.java

@@ -3,10 +3,10 @@ package com.sismics.docs.core.model.jpa;
 import java.io.Serializable;
 import java.util.Date;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Vocabulary.java

@@ -1,9 +1,9 @@
 package com.sismics.docs.core.model.jpa;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
-import javax.persistence.Entity;
+import jakarta.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Table;
 
 import com.google.common.base.MoreObjects;
 

docs-core/src/main/java/com/sismics/docs/core/model/jpa/Webhook.java

@@ -3,7 +3,7 @@ package com.sismics.docs.core.model.jpa;
 import com.google.common.base.MoreObjects;
 import com.sismics.docs.core.constant.WebhookEvent;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Date;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/service/FileService.java

@@ -69,13 +69,18 @@ public class FileService extends AbstractScheduledService {
         return Scheduler.newFixedDelaySchedule(0, 5, TimeUnit.SECONDS);
     }
 
+    public Path createTemporaryFile() throws IOException {
+        return createTemporaryFile(null);
+    }
+
     /**
      * Create a temporary file.
      *
+     * @param name Wanted file name
      * @return New temporary file
      */
-    public Path createTemporaryFile() throws IOException {
+    public Path createTemporaryFile(String name) throws IOException {
-        Path path = Files.createTempFile("sismics_docs", null);
+        Path path = Files.createTempFile("sismics_docs", name);
         referenceSet.add(new TemporaryPathReference(path, referenceQueue));
         return path;
     }

docs-core/src/main/java/com/sismics/docs/core/service/FileSizeService.java

@@ -0,0 +1,78 @@
+package com.sismics.docs.core.service;
+
+import com.google.common.util.concurrent.AbstractScheduledService;
+import com.sismics.docs.core.dao.FileDao;
+import com.sismics.docs.core.dao.UserDao;
+import com.sismics.docs.core.model.jpa.File;
+import com.sismics.docs.core.model.jpa.User;
+import com.sismics.docs.core.util.FileUtil;
+import com.sismics.docs.core.util.TransactionUtil;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+/**
+ * Service that retrieve files sizes when they are not in the database.
+ */
+public class FileSizeService extends AbstractScheduledService {
+    /**
+     * Logger.
+     */
+    private static final Logger log = LoggerFactory.getLogger(FileSizeService.class);
+
+    public FileSizeService() {
+    }
+
+    @Override
+    protected void startUp() {
+        log.info("File size service starting up");
+    }
+
+    @Override
+    protected void shutDown() {
+        log.info("File size service shutting down");
+    }
+
+    private static final int BATCH_SIZE = 30;
+    
+    @Override
+    protected void runOneIteration() {
+        try {
+            TransactionUtil.handle(() -> {
+                FileDao fileDao = new FileDao();
+                List<File> files = fileDao.getFilesWithUnknownSize(BATCH_SIZE);
+                for(File file : files) {
+                    processFile(file);
+                }
+                if(files.size() < BATCH_SIZE) {
+                    log.info("No more file to process, stopping the service");
+                    stopAsync();
+                }
+            });
+        } catch (Throwable e) {
+            log.error("Exception during file service iteration", e);
+        }
+    }
+
+    void processFile(File file) {
+        UserDao userDao = new UserDao();
+        User user = userDao.getById(file.getUserId());
+        if(user == null) {
+            return;
+        }
+
+        long fileSize = FileUtil.getFileSize(file.getId(), user);
+        if(fileSize != File.UNKNOWN_SIZE){
+            FileDao fileDao = new FileDao();
+            file.setSize(fileSize);
+            fileDao.update(file);
+        }
+    }
+
+    @Override
+    protected Scheduler scheduler() {
+        return Scheduler.newFixedDelaySchedule(0, 1, TimeUnit.MINUTES);
+    }
+}

docs-core/src/main/java/com/sismics/docs/core/service/InboxService.java

@@ -1,14 +1,11 @@
 package com.sismics.docs.core.service;
 
-import com.google.common.collect.Lists;
-import com.google.common.collect.Sets;
 import com.google.common.util.concurrent.AbstractScheduledService;
 import com.sismics.docs.core.constant.ConfigType;
 import com.sismics.docs.core.dao.TagDao;
 import com.sismics.docs.core.dao.criteria.TagCriteria;
 import com.sismics.docs.core.dao.dto.TagDto;
 import com.sismics.docs.core.event.DocumentCreatedAsyncEvent;
-import com.sismics.docs.core.model.jpa.Config;
 import com.sismics.docs.core.model.jpa.Document;
 import com.sismics.docs.core.model.jpa.Tag;
 import com.sismics.docs.core.util.ConfigUtil;
@@ -18,7 +15,7 @@ import com.sismics.docs.core.util.TransactionUtil;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 import com.sismics.util.EmailUtil;
 import com.sismics.util.context.ThreadLocalContext;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -85,7 +82,7 @@ public class InboxService extends AbstractScheduledService {
             lastSyncDate = new Date();
             lastSyncMessageCount = 0;
             try {
-                HashMap<String, String> tagsNameToId = getAllTags();
+                Map<String, String> tagsNameToId = getAllTags();
 
                 inbox = openInbox();
                 Message[] messages = inbox.search(new FlagTerm(new Flags(Flags.Flag.SEEN), false));
@@ -159,6 +156,7 @@ public class InboxService extends AbstractScheduledService {
         String port = ConfigUtil.getConfigStringValue(ConfigType.INBOX_PORT);
         properties.put("mail.imap.host", ConfigUtil.getConfigStringValue(ConfigType.INBOX_HOSTNAME));
         properties.put("mail.imap.port", port);
+        properties.setProperty("mail.imap.starttls.enable", ConfigUtil.getConfigStringValue(ConfigType.INBOX_STARTTLS).toString());
         boolean isSsl = "993".equals(port);
         properties.put("mail.imap.ssl.enable", String.valueOf(isSsl));
         properties.setProperty("mail.imap.socketFactory.class",
@@ -192,7 +190,7 @@ public class InboxService extends AbstractScheduledService {
      * @param message Message
      * @throws Exception e
      */
-    private void importMessage(Message message, HashMap<String, String> tags) throws Exception {
+    private void importMessage(Message message, Map<String, String> tags) throws Exception {
         log.info("Importing message: " + message.getSubject());
 
         // Parse the mail
@@ -273,16 +271,16 @@ public class InboxService extends AbstractScheduledService {
     /**
      * Fetches a HashMap with all tag names as keys and their respective ids as values.
      *
-     * @return HashMap with all tags or null if not enabled
+     * @return Map with all tags or null if not enabled
      */
-    private HashMap<String, String> getAllTags() {
+    private Map<String, String> getAllTags() {
         if (!ConfigUtil.getConfigBooleanValue(ConfigType.INBOX_AUTOMATIC_TAGS)) {
             return null;
         }
         TagDao tagDao = new TagDao();
         List<TagDto> tags = tagDao.findByCriteria(new TagCriteria().setTargetIdList(null), new SortCriteria(1, true));
 
-        HashMap<String, String> tagsNameToId = new HashMap<>();
+        Map<String, String> tagsNameToId = new HashMap<>();
         for (TagDto tagDto : tags) {
             tagsNameToId.put(tagDto.getName(), tagDto.getId());
         }

docs-core/src/main/java/com/sismics/docs/core/util/ActionUtil.java

@@ -9,7 +9,7 @@ import com.sismics.docs.core.util.action.RemoveTagAction;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
 
 /**
  * Action utilities.

docs-core/src/main/java/com/sismics/docs/core/util/AuditLogUtil.java

@@ -6,7 +6,7 @@ import com.sismics.docs.core.model.jpa.AuditLog;
 import com.sismics.docs.core.model.jpa.Loggable;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 
 /**
  * Audit log utilities.

docs-core/src/main/java/com/sismics/docs/core/util/ConfigUtil.java

@@ -8,13 +8,12 @@ import java.util.ResourceBundle;
 
 /**
  * Configuration parameter utilities.
- * 
+ *
- * @author jtremeaux
  */
 public class ConfigUtil {
     /**
      * Returns the textual value of a configuration parameter.
-     * 
+     *
      * @param configType Type of the configuration parameter
      * @return Textual value of the configuration parameter
      * @throws IllegalStateException Configuration parameter undefined
@@ -30,7 +29,7 @@ public class ConfigUtil {
 
     /**
      * Returns the configuration resource bundle.
-     * 
+     *
      * @return Resource bundle
      */
     public static ResourceBundle getConfigBundle() {
@@ -39,14 +38,14 @@ public class ConfigUtil {
 
     /**
      * Returns the integer value of a configuration parameter.
-     * 
+     *
      * @param configType Type of the configuration parameter
      * @return Integer value of the configuration parameter
      * @throws IllegalStateException Configuration parameter undefined
      */
     public static int getConfigIntegerValue(ConfigType configType) {
         String value = getConfigStringValue(configType);
-        
+
         return Integer.parseInt(value);
     }
 
@@ -65,14 +64,28 @@ public class ConfigUtil {
 
     /**
      * Returns the boolean value of a configuration parameter.
-     * 
+     *
      * @param configType Type of the configuration parameter
      * @return Boolean value of the configuration parameter
      * @throws IllegalStateException Configuration parameter undefined
      */
     public static boolean getConfigBooleanValue(ConfigType configType) {
         String value = getConfigStringValue(configType);
-        
         return Boolean.parseBoolean(value);
     }
+
+    /**
+     * Returns the boolean value of a configuration parameter with a default value.
+     *
+     * @param configType Type of the configuration parameter
+     * @param defaultValue Default value to return if the configuration parameter is undefined
+     * @return Boolean value of the configuration parameter
+     */
+    public static boolean getConfigBooleanValue(ConfigType configType, boolean defaultValue) {
+        try {
+            return getConfigBooleanValue(configType);
+        } catch (IllegalStateException e) {
+            return defaultValue;
+        }
+    }
 }

docs-core/src/main/java/com/sismics/docs/core/util/DirectoryUtil.java

@@ -5,7 +5,7 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import com.sismics.util.EnvironmentUtil;
 

docs-core/src/main/java/com/sismics/docs/core/util/FileUtil.java

@@ -1,6 +1,5 @@
 package com.sismics.docs.core.util;
 
-import com.google.common.base.Charsets;
 import com.google.common.base.Strings;
 import com.google.common.collect.Lists;
 import com.google.common.io.CharStreams;
@@ -17,7 +16,10 @@ import com.sismics.util.Scalr;
 import com.sismics.util.context.ThreadLocalContext;
 import com.sismics.util.io.InputStreamReaderThread;
 import com.sismics.util.mime.MimeTypeUtil;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.CountingInputStream;
+import org.apache.commons.io.output.NullOutputStream;
+import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -28,6 +30,7 @@ import java.awt.image.BufferedImage;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.*;
@@ -46,7 +49,7 @@ public class FileUtil {
     /**
      * File ID of files currently being processed.
      */
-    private static Set<String> processingFileSet = Collections.synchronizedSet(new HashSet<>());
+    private static final Set<String> processingFileSet = Collections.synchronizedSet(new HashSet<>());
     
     /**
      * Optical character recognition on an image.
@@ -76,7 +79,7 @@ public class FileUtil {
 
         // Consume the data as text
         try (InputStream is = process.getInputStream()) {
-            return CharStreams.toString(new InputStreamReader(is, Charsets.UTF_8));
+            return CharStreams.toString(new InputStreamReader(is, StandardCharsets.UTF_8));
         }
     }
 
@@ -149,6 +152,7 @@ public class FileUtil {
         file.setName(StringUtils.abbreviate(name, 200));
         file.setMimeType(mimeType);
         file.setUserId(userId);
+        file.setSize(fileSize);
 
         // Get files of this document
         FileDao fileDao = new FileDao();
@@ -240,4 +244,31 @@ public class FileUtil {
     public static boolean isProcessingFile(String fileId) {
         return processingFileSet.contains(fileId);
     }
+
+    /**
+     * Get the size of a file on disk.
+     *
+     * @param fileId the file id
+     * @param user   the file owner
+     * @return the size or -1 if something went wrong
+     */
+    public static long getFileSize(String fileId, User user) {
+        // To get the size we copy the decrypted content into a null output stream
+        // and count the copied byte size.
+        Path storedFile = DirectoryUtil.getStorageDirectory().resolve(fileId);
+        if (! Files.exists(storedFile)) {
+            log.debug("File does not exist " + fileId);
+            return File.UNKNOWN_SIZE;
+        }
+        try (InputStream fileInputStream = Files.newInputStream(storedFile);
+             InputStream inputStream = EncryptionUtil.decryptInputStream(fileInputStream, user.getPrivateKey());
+             CountingInputStream countingInputStream = new CountingInputStream(inputStream);
+        ) {
+            IOUtils.copy(countingInputStream, NullOutputStream.NULL_OUTPUT_STREAM);
+            return countingInputStream.getByteCount();
+        } catch (Exception e) {
+            log.debug("Can't find size of file " + fileId, e);
+            return File.UNKNOWN_SIZE;
+        }
+    }
 }

docs-core/src/main/java/com/sismics/docs/core/util/MetadataUtil.java

@@ -10,9 +10,9 @@ import com.sismics.docs.core.dao.dto.MetadataDto;
 import com.sismics.docs.core.model.jpa.DocumentMetadata;
 import com.sismics.docs.core.util.jpa.SortCriteria;
 
-import javax.json.Json;
+import jakarta.json.Json;
-import javax.json.JsonArrayBuilder;
+import jakarta.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.JsonObjectBuilder;
 import java.text.MessageFormat;
 import java.util.List;
 import java.util.Map;

docs-core/src/main/java/com/sismics/docs/core/util/RoutingUtil.java

@@ -19,10 +19,10 @@ import com.sismics.docs.core.model.jpa.Document;
 import com.sismics.docs.core.model.jpa.RouteModel;
 import com.sismics.util.context.ThreadLocalContext;
 
-import javax.json.Json;
+import jakarta.json.Json;
-import javax.json.JsonArray;
+import jakarta.json.JsonArray;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
-import javax.json.JsonReader;
+import jakarta.json.JsonReader;
 import java.io.StringReader;
 import java.util.List;
 

docs-core/src/main/java/com/sismics/docs/core/util/TransactionUtil.java

@@ -5,8 +5,8 @@ import com.sismics.util.jpa.EMF;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.EntityTransaction;
+import jakarta.persistence.EntityTransaction;
 
 /**
  * Database transaction utils.

docs-core/src/main/java/com/sismics/docs/core/util/action/Action.java

@@ -2,7 +2,7 @@ package com.sismics.docs.core.util.action;
 
 import com.sismics.docs.core.dao.dto.DocumentDto;
 
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
 
 /**
  * Base action interface.

docs-core/src/main/java/com/sismics/docs/core/util/action/AddTagAction.java

@@ -6,7 +6,7 @@ import com.sismics.docs.core.dao.criteria.TagCriteria;
 import com.sismics.docs.core.dao.dto.DocumentDto;
 import com.sismics.docs.core.dao.dto.TagDto;
 
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
 import java.util.List;
 import java.util.Set;
 

docs-core/src/main/java/com/sismics/docs/core/util/action/ProcessFilesAction.java

@@ -13,7 +13,7 @@ import com.sismics.util.context.ThreadLocalContext;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
 import java.nio.file.Path;
 import java.util.List;
 

docs-core/src/main/java/com/sismics/docs/core/util/action/RemoveTagAction.java

@@ -6,7 +6,7 @@ import com.sismics.docs.core.dao.criteria.TagCriteria;
 import com.sismics.docs.core.dao.dto.DocumentDto;
 import com.sismics.docs.core.dao.dto.TagDto;
 
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
 import java.util.List;
 import java.util.Set;
 

docs-core/src/main/java/com/sismics/docs/core/util/action/TagAction.java

@@ -4,7 +4,7 @@ import com.sismics.docs.core.dao.TagDao;
 import com.sismics.docs.core.dao.criteria.TagCriteria;
 import com.sismics.docs.core.dao.dto.TagDto;
 
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
 import java.util.List;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/util/authentication/LdapAuthenticationHandler.java

@@ -13,10 +13,9 @@ import org.apache.directory.api.ldap.model.entry.Attribute;
 import org.apache.directory.api.ldap.model.entry.Entry;
 import org.apache.directory.api.ldap.model.entry.Value;
 import org.apache.directory.api.ldap.model.message.SearchScope;
-import org.apache.directory.ldap.client.api.DefaultLdapConnectionFactory;
+import org.apache.directory.ldap.client.api.LdapConnection;
 import org.apache.directory.ldap.client.api.LdapConnectionConfig;
-import org.apache.directory.ldap.client.api.LdapConnectionPool;
+import org.apache.directory.ldap.client.api.LdapNetworkConnection;
-import org.apache.directory.ldap.client.api.ValidatingPoolableLdapConnectionFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -35,59 +34,41 @@ public class LdapAuthenticationHandler implements AuthenticationHandler {
     private static final Logger log = LoggerFactory.getLogger(LdapAuthenticationHandler.class);
 
     /**
-     * LDAP connection pool.
+     * Get a LDAP connection.
+     * @return LdapConnection
      */
-    private static LdapConnectionPool pool;
+    private LdapConnection getConnection() {
-
-    /**
-     * Reset the LDAP pool.
-     */
-    public static void reset() {
-        if (pool != null) {
-            try {
-                pool.close();
-            } catch (Exception e) {
-                // NOP
-            }
-        }
-        pool = null;
-    }
-
-    /**
-     * Initialize the LDAP pool.
-     */
-    private static void init() {
         ConfigDao configDao = new ConfigDao();
         Config ldapEnabled = configDao.getById(ConfigType.LDAP_ENABLED);
-        if (pool != null || ldapEnabled == null || !Boolean.parseBoolean(ldapEnabled.getValue())) {
+        if (ldapEnabled == null || !Boolean.parseBoolean(ldapEnabled.getValue())) {
-            return;
+            return null;
         }
 
         LdapConnectionConfig config = new LdapConnectionConfig();
         config.setLdapHost(ConfigUtil.getConfigStringValue(ConfigType.LDAP_HOST));
         config.setLdapPort(ConfigUtil.getConfigIntegerValue(ConfigType.LDAP_PORT));
+        config.setUseSsl(ConfigUtil.getConfigBooleanValue(ConfigType.LDAP_USESSL));
         config.setName(ConfigUtil.getConfigStringValue(ConfigType.LDAP_ADMIN_DN));
         config.setCredentials(ConfigUtil.getConfigStringValue(ConfigType.LDAP_ADMIN_PASSWORD));
 
-        DefaultLdapConnectionFactory factory = new DefaultLdapConnectionFactory(config);
+        return new LdapNetworkConnection(config);
-        pool = new LdapConnectionPool(new ValidatingPoolableLdapConnectionFactory(factory), null);
     }
 
     @Override
     public User authenticate(String username, String password) {
-        init();
-        if (pool == null) {
-            return null;
-        }
-
         // Fetch and authenticate the user
         Entry userEntry;
-        try {
+        try (LdapConnection ldapConnection = getConnection()) {
-            EntryCursor cursor = pool.getConnection().search(ConfigUtil.getConfigStringValue(ConfigType.LDAP_BASE_DN),
+            if (ldapConnection == null) {
+                return null;
+            }
+            ldapConnection.bind();
+
+            EntryCursor cursor = ldapConnection.search(ConfigUtil.getConfigStringValue(ConfigType.LDAP_BASE_DN),
                     ConfigUtil.getConfigStringValue(ConfigType.LDAP_FILTER).replace("USERNAME", username), SearchScope.SUBTREE);
             if (cursor.next()) {
                 userEntry = cursor.get();
-                pool.getConnection().bind(userEntry.getDn(), password);
+                ldapConnection.bind(userEntry.getDn(), password);
             } else {
                 // User not found
                 return null;

docs-core/src/main/java/com/sismics/docs/core/util/format/FormatHandlerUtil.java

@@ -3,7 +3,6 @@ package com.sismics.docs.core.util.format;
 import com.google.common.collect.Lists;
 import com.sismics.util.ClasspathScanner;
 
-import java.lang.reflect.InvocationTargetException;
 import java.util.List;
 
 /**

docs-core/src/main/java/com/sismics/docs/core/util/format/ImageFormatHandler.java

@@ -3,6 +3,8 @@ package com.sismics.docs.core.util.format;
 import com.google.common.io.Closer;
 import com.sismics.docs.core.constant.Constants;
 import com.sismics.docs.core.util.FileUtil;
+import com.sismics.docs.core.util.ConfigUtil;
+import com.sismics.docs.core.constant.ConfigType;
 import com.sismics.util.mime.MimeType;
 import org.apache.pdfbox.io.MemoryUsageSetting;
 import org.apache.pdfbox.pdmodel.PDDocument;
@@ -22,7 +24,6 @@ import java.nio.file.Path;
 /**
  * Image format handler.
  *
- * @author bgamard
  */
 public class ImageFormatHandler implements FormatHandler {
     /**
@@ -45,7 +46,7 @@ public class ImageFormatHandler implements FormatHandler {
 
     @Override
     public String extractContent(String language, Path file) throws Exception {
-        if (language == null) {
+        if (language == null || !ConfigUtil.getConfigBooleanValue(ConfigType.OCR_ENABLED, true)) {
             return null;
         }
 

docs-core/src/main/java/com/sismics/docs/core/util/format/PdfFormatHandler.java

@@ -2,6 +2,8 @@ package com.sismics.docs.core.util.format;
 
 import com.google.common.io.Closer;
 import com.sismics.docs.core.util.FileUtil;
+import com.sismics.docs.core.util.ConfigUtil;
+import com.sismics.docs.core.constant.ConfigType;
 import com.sismics.util.mime.MimeType;
 import org.apache.pdfbox.io.MemoryUsageSetting;
 import org.apache.pdfbox.multipdf.PDFMergerUtility;
@@ -53,7 +55,7 @@ public class PdfFormatHandler implements FormatHandler {
         }
 
         // No text content, try to OCR it
-        if (language != null && content != null && content.trim().isEmpty()) {
+        if (language != null && content != null && content.trim().isEmpty() && ConfigUtil.getConfigBooleanValue(ConfigType.OCR_ENABLED, true)) {
             StringBuilder sb = new StringBuilder();
             try (InputStream inputStream = Files.newInputStream(file);
                  PDDocument pdfDocument = PDDocument.load(inputStream)) {

docs-core/src/main/java/com/sismics/docs/core/util/format/TextPlainFormatHandler.java

@@ -1,6 +1,5 @@
 package com.sismics.docs.core.util.format;
 
-import com.google.common.base.Charsets;
 import com.google.common.io.Closer;
 import com.lowagie.text.*;
 import com.lowagie.text.pdf.PdfWriter;
@@ -11,6 +10,7 @@ import org.apache.pdfbox.pdmodel.PDDocument;
 
 import java.awt.image.BufferedImage;
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 
@@ -33,7 +33,7 @@ public class TextPlainFormatHandler implements FormatHandler {
         PdfWriter.getInstance(output, pdfOutputStream);
 
         output.open();
-        String content = new String(Files.readAllBytes(file), Charsets.UTF_8);
+        String content = Files.readString(file, StandardCharsets.UTF_8);
         Font font = FontFactory.getFont("LiberationMono-Regular");
         Paragraph paragraph = new Paragraph(content, font);
         paragraph.setAlignment(Element.ALIGN_LEFT);
@@ -46,7 +46,7 @@ public class TextPlainFormatHandler implements FormatHandler {
 
     @Override
     public String extractContent(String language, Path file) throws Exception {
-        return new String(Files.readAllBytes(file), "UTF-8");
+        return Files.readString(file, StandardCharsets.UTF_8);
     }
 
     @Override

docs-core/src/main/java/com/sismics/docs/core/util/format/VideoFormatHandler.java

@@ -1,6 +1,5 @@
 package com.sismics.docs.core.util.format;
 
-import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
 import com.google.common.io.ByteStreams;
 import com.google.common.io.Closer;
@@ -13,6 +12,7 @@ import javax.imageio.ImageIO;
 import java.awt.image.BufferedImage;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.List;
@@ -65,7 +65,7 @@ public class VideoFormatHandler implements FormatHandler {
 
         // Consume the data as a string
         try (InputStream is = process.getInputStream()) {
-            return new String(ByteStreams.toByteArray(is), Charsets.UTF_8);
+            return new String(ByteStreams.toByteArray(is), StandardCharsets.UTF_8);
         } catch (Exception e) {
             return null;
         }

docs-core/src/main/java/com/sismics/docs/core/util/indexing/LuceneIndexingHandler.java

@@ -26,9 +26,18 @@ import org.apache.lucene.analysis.standard.StandardAnalyzer;
 import org.apache.lucene.document.Field;
 import org.apache.lucene.document.StringField;
 import org.apache.lucene.document.TextField;
-import org.apache.lucene.index.*;
+import org.apache.lucene.index.CheckIndex;
+import org.apache.lucene.index.ConcurrentMergeScheduler;
+import org.apache.lucene.index.DirectoryReader;
+import org.apache.lucene.index.IndexWriter;
+import org.apache.lucene.index.IndexWriterConfig;
+import org.apache.lucene.index.Term;
 import org.apache.lucene.queryparser.simple.SimpleQueryParser;
-import org.apache.lucene.search.*;
+import org.apache.lucene.search.BooleanClause;
+import org.apache.lucene.search.BooleanQuery;
+import org.apache.lucene.search.IndexSearcher;
+import org.apache.lucene.search.ScoreDoc;
+import org.apache.lucene.search.TopDocs;
 import org.apache.lucene.search.highlight.Highlighter;
 import org.apache.lucene.search.highlight.QueryScorer;
 import org.apache.lucene.search.highlight.SimpleHTMLEncoder;
@@ -47,7 +56,12 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.sql.Timestamp;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
 
 /**
  * Lucene indexing handler.
@@ -242,34 +256,28 @@ public class LuceneIndexingHandler implements IndexingHandler {
 
         StringBuilder sb = new StringBuilder("select distinct d.DOC_ID_C c0, d.DOC_TITLE_C c1, d.DOC_DESCRIPTION_C c2, d.DOC_CREATEDATE_D c3, d.DOC_LANGUAGE_C c4, d.DOC_IDFILE_C, ");
         sb.append(" s.count c5, ");
-        sb.append(" f.count c6, ");
         sb.append(" rs2.RTP_ID_C c7, rs2.RTP_NAME_C, d.DOC_UPDATEDATE_D c8 ");
         sb.append(" from T_DOCUMENT d ");
         sb.append(" left join (SELECT count(s.SHA_ID_C) count, ac.ACL_SOURCEID_C " +
                 "   FROM T_SHARE s, T_ACL ac " +
                 "   WHERE ac.ACL_TARGETID_C = s.SHA_ID_C AND ac.ACL_DELETEDATE_D IS NULL AND " +
-                "         s.SHA_DELETEDATE_D IS NULL group by ac.ACL_SOURCEID_C) s on s.ACL_SOURCEID_C = d.DOC_ID_C " +
+                "         s.SHA_DELETEDATE_D IS NULL group by ac.ACL_SOURCEID_C) s on s.ACL_SOURCEID_C = d.DOC_ID_C ");
-                "  left join (SELECT count(f.FIL_ID_C) count, f.FIL_IDDOC_C " +
-                "   FROM T_FILE f " +
-                "   WHERE f.FIL_DELETEDATE_D is null group by f.FIL_IDDOC_C) f on f.FIL_IDDOC_C = d.DOC_ID_C ");
         sb.append(" left join (select rs.*, rs3.idDocument " +
                 "from T_ROUTE_STEP rs " +
                 "join (select r.RTE_IDDOCUMENT_C idDocument, rs.RTP_IDROUTE_C idRoute, min(rs.RTP_ORDER_N) minOrder from T_ROUTE_STEP rs join T_ROUTE r on r.RTE_ID_C = rs.RTP_IDROUTE_C and r.RTE_DELETEDATE_D is null where rs.RTP_DELETEDATE_D is null and rs.RTP_ENDDATE_D is null group by rs.RTP_IDROUTE_C, r.RTE_IDDOCUMENT_C) rs3 on rs.RTP_IDROUTE_C = rs3.idRoute and rs.RTP_ORDER_N = rs3.minOrder " +
                 "where rs.RTP_IDTARGET_C in (:targetIdList)) rs2 on rs2.idDocument = d.DOC_ID_C ");
 
         // Add search criterias
-        if (criteria.getTargetIdList() != null) {
+        if (!SecurityUtil.skipAclCheck(criteria.getTargetIdList())) {
-            if (!SecurityUtil.skipAclCheck(criteria.getTargetIdList())) {
+            // Read permission is enough for searching
-                // Read permission is enough for searching
+            sb.append(" left join T_ACL a on a.ACL_TARGETID_C in (:targetIdList) and a.ACL_SOURCEID_C = d.DOC_ID_C and a.ACL_PERM_C = 'READ' and a.ACL_DELETEDATE_D is null ");
-                sb.append(" left join T_ACL a on a.ACL_TARGETID_C in (:targetIdList) and a.ACL_SOURCEID_C = d.DOC_ID_C and a.ACL_PERM_C = 'READ' and a.ACL_DELETEDATE_D is null ");
+            sb.append(" left join T_DOCUMENT_TAG dta on dta.DOT_IDDOCUMENT_C = d.DOC_ID_C and dta.DOT_DELETEDATE_D is null ");
-                sb.append(" left join T_DOCUMENT_TAG dta on dta.DOT_IDDOCUMENT_C = d.DOC_ID_C and dta.DOT_DELETEDATE_D is null ");
+            sb.append(" left join T_ACL a2 on a2.ACL_TARGETID_C in (:targetIdList) and a2.ACL_SOURCEID_C = dta.DOT_IDTAG_C and a2.ACL_PERM_C = 'READ' and a2.ACL_DELETEDATE_D is null ");
-                sb.append(" left join T_ACL a2 on a2.ACL_TARGETID_C in (:targetIdList) and a2.ACL_SOURCEID_C = dta.DOT_IDTAG_C and a2.ACL_PERM_C = 'READ' and a2.ACL_DELETEDATE_D is null ");
+            criteriaList.add("(a.ACL_ID_C is not null or a2.ACL_ID_C is not null)");
-                criteriaList.add("(a.ACL_ID_C is not null or a2.ACL_ID_C is not null)");
-            }
-            parameterMap.put("targetIdList", criteria.getTargetIdList());
         }
-        if (!Strings.isNullOrEmpty(criteria.getSearch()) || !Strings.isNullOrEmpty(criteria.getFullSearch())) {
+        parameterMap.put("targetIdList", criteria.getTargetIdList());
-            documentSearchMap = search(criteria.getSearch(), criteria.getFullSearch());
+        if (!Strings.isNullOrEmpty(criteria.getSimpleSearch()) || !Strings.isNullOrEmpty(criteria.getFullSearch())) {
+            documentSearchMap = search(criteria.getSimpleSearch(), criteria.getFullSearch());
             if (documentSearchMap.isEmpty()) {
                 // If the search doesn't find any document, the request should return nothing
                 documentSearchMap.put(UUID.randomUUID().toString(), null);
@@ -295,11 +303,11 @@ public class LuceneIndexingHandler implements IndexingHandler {
             criteriaList.add("d.DOC_UPDATEDATE_D <= :updateDateMax");
             parameterMap.put("updateDateMax", criteria.getUpdateDateMax());
         }
-        if (criteria.getTitle() != null) {
+        if (!criteria.getTitleList().isEmpty()) {
-            criteriaList.add("d.DOC_TITLE_C = :title");
+            criteriaList.add("d.DOC_TITLE_C in :title");
-            parameterMap.put("title", criteria.getTitle());
+            parameterMap.put("title", criteria.getTitleList());
         }
-        if (criteria.getTagIdList() != null && !criteria.getTagIdList().isEmpty()) {
+        if (!criteria.getTagIdList().isEmpty()) {
             int index = 0;
             for (List<String> tagIdList : criteria.getTagIdList()) {
                 List<String> tagCriteriaList = Lists.newArrayList();
@@ -312,7 +320,7 @@ public class LuceneIndexingHandler implements IndexingHandler {
                 criteriaList.add("(" + Joiner.on(" OR ").join(tagCriteriaList) + ")");
             }
         }
-        if (criteria.getExcludedTagIdList() != null && !criteria.getExcludedTagIdList().isEmpty()) {
+        if (!criteria.getExcludedTagIdList().isEmpty()) {
             int index = 0;
             for (List<String> tagIdList : criteria.getExcludedTagIdList()) {
                 List<String> tagCriteriaList = Lists.newArrayList();
@@ -347,10 +355,8 @@ public class LuceneIndexingHandler implements IndexingHandler {
 
         criteriaList.add("d.DOC_DELETEDATE_D is null");
 
-        if (!criteriaList.isEmpty()) {
+        sb.append(" where ");
-            sb.append(" where ");
+        sb.append(Joiner.on(" and ").join(criteriaList));
-            sb.append(Joiner.on(" and ").join(criteriaList));
-        }
 
         // Perform the search
         QueryParam queryParam = new QueryParam(sb.toString(), parameterMap);
@@ -369,8 +375,6 @@ public class LuceneIndexingHandler implements IndexingHandler {
             documentDto.setFileId((String) o[i++]);
             Number shareCount = (Number) o[i++];
             documentDto.setShared(shareCount != null && shareCount.intValue() > 0);
-            Number fileCount = (Number) o[i++];
-            documentDto.setFileCount(fileCount == null ? 0 : fileCount.intValue());
             documentDto.setActiveRoute(o[i++] != null);
             documentDto.setCurrentStepName((String) o[i++]);
             documentDto.setUpdateTimestamp(((Timestamp) o[i]).getTime());
@@ -408,14 +412,14 @@ public class LuceneIndexingHandler implements IndexingHandler {
     /**
      * Fulltext search in files and documents.
      *
-     * @param searchQuery Search query on metadatas
+     * @param simpleSearchQuery Search query on metadatas
      * @param fullSearchQuery Search query on all fields
      * @return Map of document IDs as key and highlight as value
      * @throws Exception e
      */
-    private Map<String, String> search(String searchQuery, String fullSearchQuery) throws Exception {
+    private Map<String, String> search(String simpleSearchQuery, String fullSearchQuery) throws Exception {
         // The fulltext query searches in all fields
-        searchQuery = searchQuery + " " + fullSearchQuery;
+        String searchQuery = simpleSearchQuery + " " + fullSearchQuery;
 
         // Build search query
         Analyzer analyzer = new StandardAnalyzer();

docs-core/src/main/java/com/sismics/docs/core/util/jpa/PaginatedLists.java

@@ -1,6 +1,6 @@
 package com.sismics.docs.core.util.jpa;
 
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.util.List;
 
 /**
@@ -68,7 +68,7 @@ public class PaginatedLists {
     }
 
     /**
-     * Executes a query and returns the data of the currunt page.
+     * Executes a query and returns the data of the current page.
      * 
      * @param paginatedList Paginated list object containing parameters, and into which results are added by side effects
      * @param queryParam Query parameters
@@ -82,18 +82,6 @@ public class PaginatedLists {
         q.setMaxResults(paginatedList.getLimit());
         return q.getResultList();
     }
-    
-    /**
-     * Executes a paginated request with 2 native queries (one to count the number of results, and one to return the page).
-     * 
-     * @param paginatedList Paginated list object containing parameters, and into which results are added by side effects
-     * @param queryParam Query parameters
-     * @return List of results
-     */
-    public static <E> List<Object[]> executePaginatedQuery(PaginatedList<E> paginatedList, QueryParam queryParam) {
-        executeCountQuery(paginatedList, queryParam);
-        return executeResultQuery(paginatedList, queryParam);
-    }
 
     /**
      * Executes a paginated request with 2 native queries (one to count the number of results, and one to return the page).

docs-core/src/main/java/com/sismics/docs/core/util/jpa/QueryUtil.java

@@ -2,8 +2,8 @@ package com.sismics.docs.core.util.jpa;
 
 import java.util.Map.Entry;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 
 import com.sismics.util.context.ThreadLocalContext;
 

docs-core/src/main/java/com/sismics/util/EmailUtil.java

@@ -17,9 +17,9 @@ import org.jsoup.Jsoup;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.json.Json;
+import jakarta.json.Json;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
-import javax.json.JsonReader;
+import jakarta.json.JsonReader;
 import javax.mail.Message;
 import javax.mail.MessagingException;
 import javax.mail.Multipart;
@@ -29,6 +29,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
 import java.io.StringWriter;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
@@ -87,12 +88,12 @@ public class EmailUtil {
         try {
             // Build email headers
             HtmlEmail email = new HtmlEmail();
-            email.setCharset("UTF-8");
+            email.setCharset(StandardCharsets.UTF_8.name());
             ConfigDao configDao = new ConfigDao();
 
             // Hostname
             String envHostname = System.getenv(Constants.SMTP_HOSTNAME_ENV);
-            if (envHostname == null) {
+            if (Strings.isNullOrEmpty(envHostname)) {
                 email.setHostName(ConfigUtil.getConfigStringValue(ConfigType.SMTP_HOSTNAME));
             } else {
                 email.setHostName(envHostname);
@@ -101,7 +102,7 @@ public class EmailUtil {
             // Port
             int port = ConfigUtil.getConfigIntegerValue(ConfigType.SMTP_PORT);
             String envPort = System.getenv(Constants.SMTP_PORT_ENV);
-            if (envPort != null) {
+            if (!Strings.isNullOrEmpty(envPort)) {
                 port = Integer.valueOf(envPort);
             }
             email.setSmtpPort(port);
@@ -114,7 +115,7 @@ public class EmailUtil {
             // Username and password
             String envUsername = System.getenv(Constants.SMTP_USERNAME_ENV);
             String envPassword = System.getenv(Constants.SMTP_PASSWORD_ENV);
-            if (envUsername == null || envPassword == null) {
+            if (Strings.isNullOrEmpty(envUsername) || Strings.isNullOrEmpty(envPassword)) {
                 Config usernameConfig = configDao.getById(ConfigType.SMTP_USERNAME);
                 Config passwordConfig = configDao.getById(ConfigType.SMTP_PASSWORD);
                 if (usernameConfig != null && passwordConfig != null) {

docs-core/src/main/java/com/sismics/util/ImageUtil.java

@@ -1,6 +1,5 @@
 package com.sismics.util;
 
-import com.google.common.base.Charsets;
 import com.google.common.hash.Hashing;
 
 import javax.imageio.IIOImage;
@@ -13,6 +12,7 @@ import java.awt.image.BufferedImage;
 import java.awt.image.WritableRaster;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
 
 /**
@@ -80,7 +80,7 @@ public class ImageUtil {
         }
 
         return Hashing.md5().hashString(
-                email.trim().toLowerCase(), Charsets.UTF_8)
+                email.trim().toLowerCase(), StandardCharsets.UTF_8)
                 .toString();
     }
 

docs-core/src/main/java/com/sismics/util/JsonUtil.java

@@ -1,7 +1,7 @@
 package com.sismics.util;
 
-import javax.json.Json;
+import jakarta.json.Json;
-import javax.json.JsonValue;
+import jakarta.json.JsonValue;
 
 /**
  * JSON utilities.

docs-core/src/main/java/com/sismics/util/ResourceUtil.java

@@ -8,6 +8,7 @@ import java.io.IOException;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
 import java.text.MessageFormat;
 import java.util.*;
 import java.util.jar.JarEntry;
@@ -53,7 +54,7 @@ public class ResourceUtil {
             
             // Extract the JAR path
             String jarPath = dirUrl.getPath().substring(5, dirUrl.getPath().indexOf("!"));
-            JarFile jar = new JarFile(URLDecoder.decode(jarPath, "UTF-8"));
+            JarFile jar = new JarFile(URLDecoder.decode(jarPath, StandardCharsets.UTF_8));
             Set<String> fileSet = new HashSet<String>();
             
             try {

docs-core/src/main/java/com/sismics/util/context/ThreadLocalContext.java

@@ -3,7 +3,7 @@ package com.sismics.util.context;
 import com.google.common.collect.Lists;
 import com.sismics.docs.core.model.context.AppContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.util.Iterator;
 import java.util.List;
 

docs-core/src/main/java/com/sismics/util/jpa/DbOpenHelper.java

@@ -39,7 +39,7 @@ abstract class DbOpenHelper {
     private static final Logger log = LoggerFactory.getLogger(DbOpenHelper.class);
 
     private final JdbcConnectionAccess jdbcConnectionAccess;
-    
+
     private final List<Exception> exceptions = new ArrayList<>();
 
     private Formatter formatter;
@@ -99,7 +99,7 @@ abstract class DbOpenHelper {
                 onCreate();
                 oldVersion = 0;
             }
-            
+
             // Execute update script
             ResourceBundle configBundle = ConfigUtil.getConfigBundle();
             Integer currentVersion = Integer.parseInt(configBundle.getString("db.version"));
@@ -126,7 +126,7 @@ abstract class DbOpenHelper {
 
     /**
      * Execute all upgrade scripts in ascending order for a given version.
-     * 
+     *
      * @param version Version number
      * @throws Exception e
      */
@@ -136,7 +136,7 @@ abstract class DbOpenHelper {
             return name.matches("dbupdate-" + versionString + "-\\d+\\.sql");
         });
         Collections.sort(fileNameList);
-        
+
         for (String fileName : fileNameList) {
             if (log.isInfoEnabled()) {
                 log.info(MessageFormat.format("Executing script: {0}", fileName));
@@ -145,16 +145,16 @@ abstract class DbOpenHelper {
             executeScript(is);
         }
     }
-    
+
     /**
      * Execute a SQL script. All statements must be one line only.
-     * 
+     *
      * @param inputScript Script to execute
      * @throws IOException e
      */
     private void executeScript(InputStream inputScript) throws IOException {
         List<String> lines = CharStreams.readLines(new InputStreamReader(inputScript));
-        
+
         for (String sql : lines) {
             if (Strings.isNullOrEmpty(sql) || sql.startsWith("--")) {
                 continue;
@@ -178,13 +178,13 @@ abstract class DbOpenHelper {
     }
 
     public abstract void onCreate() throws Exception;
-    
+
     public abstract void onUpgrade(int oldVersion, int newVersion) throws Exception;
-    
+
     /**
-     * Returns a List of all Exceptions which occured during the export.
+     * Returns a List of all Exceptions which occurred during the export.
      *
-     * @return A List containig the Exceptions occured during the export
+     * @return A List containing the Exceptions occurred during the export
      */
     public List<?> getExceptions() {
         return exceptions;
@@ -192,7 +192,7 @@ abstract class DbOpenHelper {
 
     /**
      * Format the output SQL statements.
-     * 
+     *
      * @param format True to format
      */
     public void setFormat(boolean format) {

docs-core/src/main/java/com/sismics/util/jpa/EMF.java

@@ -1,5 +1,6 @@
 package com.sismics.util.jpa;
 
+import com.google.common.base.Strings;
 import com.sismics.docs.core.util.DirectoryUtil;
 import org.hibernate.boot.registry.StandardServiceRegistryBuilder;
 import org.hibernate.internal.util.config.ConfigurationHelper;
@@ -7,8 +8,8 @@ import org.hibernate.service.ServiceRegistry;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.persistence.EntityManagerFactory;
+import jakarta.persistence.EntityManagerFactory;
-import javax.persistence.Persistence;
+import jakarta.persistence.Persistence;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
@@ -25,7 +26,7 @@ import java.util.Properties;
 public final class EMF {
     private static final Logger log = LoggerFactory.getLogger(EMF.class);
 
-    private static Map<Object, Object> properties;
+    private static Properties properties;
 
     private static EntityManagerFactory emfInstance;
 
@@ -58,7 +59,7 @@ public final class EMF {
         }
     }
     
-    private static Map<Object, Object> getEntityManagerProperties() {
+    private static Properties getEntityManagerProperties() {
         // Use properties file if exists
         try {
             URL hibernatePropertiesUrl = EMF.class.getResource("/hibernate.properties");
@@ -78,19 +79,24 @@ public final class EMF {
         String databaseUrl = System.getenv("DATABASE_URL");
         String databaseUsername = System.getenv("DATABASE_USER");
         String databasePassword = System.getenv("DATABASE_PASSWORD");
+        String databasePoolSize = System.getenv("DATABASE_POOL_SIZE");
+        if(databasePoolSize == null) {
+            databasePoolSize = "10";
+        }
 
         log.info("Configuring EntityManager from environment parameters");
-        Map<Object, Object> props = new HashMap<>();
+        Properties props = new Properties();
         Path dbDirectory = DirectoryUtil.getDbDirectory();
         String dbFile = dbDirectory.resolve("docs").toAbsolutePath().toString();
-        if (databaseUrl == null) {
+        if (Strings.isNullOrEmpty(databaseUrl)) {
+            log.warn("Using an embedded H2 database. Only suitable for testing purpose, not for production!");
             props.put("hibernate.connection.driver_class", "org.h2.Driver");
             props.put("hibernate.dialect", "org.hibernate.dialect.HSQLDialect");
             props.put("hibernate.connection.url", "jdbc:h2:file:" + dbFile + ";CACHE_SIZE=65536;LOCK_TIMEOUT=10000");
             props.put("hibernate.connection.username", "sa");
         } else {
             props.put("hibernate.connection.driver_class", "org.postgresql.Driver");
-            props.put("hibernate.dialect", "org.hibernate.dialect.PostgreSQL94Dialect");
+            props.put("hibernate.dialect", "org.hibernate.dialect.PostgreSQLDialect");
             props.put("hibernate.connection.url", databaseUrl);
             props.put("hibernate.connection.username", databaseUsername);
             props.put("hibernate.connection.password", databasePassword);
@@ -100,12 +106,9 @@ public final class EMF {
         props.put("hibernate.format_sql", "false");
         props.put("hibernate.max_fetch_depth", "5");
         props.put("hibernate.cache.use_second_level_cache", "false");
-        props.put("hibernate.c3p0.min_size", "1");
+        props.put("hibernate.connection.initial_pool_size", "1");
-        props.put("hibernate.c3p0.max_size", "10");
+        props.put("hibernate.connection.pool_size", databasePoolSize);
-        props.put("hibernate.c3p0.timeout", "5000");
+        props.put("hibernate.connection.pool_validation_interval", "5");
-        props.put("hibernate.c3p0.max_statements", "0");
-        props.put("hibernate.c3p0.acquire_increment", "1");
-        props.put("hibernate.c3p0.idle_test_period", "10");
         return props;
     }
     
@@ -137,4 +140,4 @@ public final class EMF {
     public static String getDriver() {
         return (String) properties.get("hibernate.connection.driver_class");
     }
-}
+}

docs-core/src/main/java/com/sismics/util/log4j/LogCriteria.java

@@ -1,6 +1,6 @@
 package com.sismics.util.log4j;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Level;
 
 /**

docs-core/src/main/java/com/sismics/util/mime/MimeType.java

@@ -13,7 +13,7 @@ public class MimeType {
     public static final String IMAGE_GIF = "image/gif";
     
     public static final String APPLICATION_ZIP = "application/zip";
-    
+
     public static final String APPLICATION_PDF = "application/pdf";
     
     public static final String OPEN_DOCUMENT_TEXT = "application/vnd.oasis.opendocument.text";

docs-core/src/main/java/com/sismics/util/mime/MimeTypeUtil.java

@@ -1,15 +1,9 @@
 package com.sismics.util.mime;
 
-import com.google.common.base.Charsets;
-import org.apache.commons.compress.utils.IOUtils;
-
 import java.io.IOException;
-import java.io.InputStream;
+import java.net.URLConnection;
-import java.io.UnsupportedEncodingException;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
 
 /**
  * Utility to check MIME types.
@@ -18,7 +12,7 @@ import java.util.zip.ZipInputStream;
  */
 public class MimeTypeUtil {
     /**
-     * Try to guess the MIME type of a file by its magic number (header).
+     * Try to guess the MIME type of a file.
      * 
      * @param file File to inspect
      * @param name File name
@@ -26,57 +20,17 @@ public class MimeTypeUtil {
      * @throws IOException e
      */
     public static String guessMimeType(Path file, String name) throws IOException {
-        String mimeType;
+        String mimeType = Files.probeContentType(file);
-        try (InputStream is = Files.newInputStream(file)) {
+
-            byte[] headerBytes = new byte[64];
+        if (mimeType == null && name != null) {
-            is.read(headerBytes);
+            mimeType = URLConnection.getFileNameMap().getContentTypeFor(name);
-            mimeType = guessMimeType(headerBytes, name);
         }
 
-        return guessOpenDocumentFormat(mimeType, file);
+        if (mimeType == null) {
-    }
+            return MimeType.DEFAULT;
-
-    /**
-     * Try to guess the MIME type of a file by its magic number (header).
-     * 
-     * @param headerBytes File header (first bytes)
-     * @param name File name
-     * @return MIME type
-     * @throws UnsupportedEncodingException e
-     */
-    public static String guessMimeType(byte[] headerBytes, String name) throws UnsupportedEncodingException {
-        String header = new String(headerBytes, "US-ASCII");
-
-        // Detect by header bytes
-        if (header.startsWith("PK")) {
-            return MimeType.APPLICATION_ZIP;
-        } else if (header.startsWith("GIF87a") || header.startsWith("GIF89a")) {
-            return MimeType.IMAGE_GIF;
-        } else if (headerBytes[0] == ((byte) 0xff) && headerBytes[1] == ((byte) 0xd8)) {
-            return MimeType.IMAGE_JPEG;
-        } else if (headerBytes[0] == ((byte) 0x89) && headerBytes[1] == ((byte) 0x50) && headerBytes[2] == ((byte) 0x4e) && headerBytes[3] == ((byte) 0x47) &&
-                headerBytes[4] == ((byte) 0x0d) && headerBytes[5] == ((byte) 0x0a) && headerBytes[6] == ((byte) 0x1a) && headerBytes[7] == ((byte) 0x0a)) {
-            return MimeType.IMAGE_PNG;
-        } else if (headerBytes[0] == ((byte) 0x25) && headerBytes[1] == ((byte) 0x50) && headerBytes[2] == ((byte) 0x44) && headerBytes[3] == ((byte) 0x46)) {
-            return MimeType.APPLICATION_PDF;
-        } else if (headerBytes[0] == ((byte) 0x00) && headerBytes[1] == ((byte) 0x00) && headerBytes[2] == ((byte) 0x00)
-                && (headerBytes[3] == ((byte) 0x14) || headerBytes[3] == ((byte) 0x18) || headerBytes[3] == ((byte) 0x20))
-                && headerBytes[4] == ((byte) 0x66) && headerBytes[5] == ((byte) 0x74) && headerBytes[6] == ((byte) 0x79) && headerBytes[7] == ((byte) 0x70)) {
-            return MimeType.VIDEO_MP4;
-        } else if (headerBytes[0] == ((byte) 0x1a) && headerBytes[1] == ((byte) 0x45) && headerBytes[2] == ((byte) 0xdf) && headerBytes[3] == ((byte) 0xa3)) {
-            return MimeType.VIDEO_WEBM;
         }
 
-        // Detect by file extension
+        return mimeType;
-        if (name != null) {
-            if (name.endsWith(".txt")) {
-                return MimeType.TEXT_PLAIN;
-            } else if (name.endsWith(".csv")) {
-                return MimeType.TEXT_CSV;
-            }
-        }
-
-        return MimeType.DEFAULT;
     }
     
     /**
@@ -113,52 +67,4 @@ public class MimeTypeUtil {
                 return "bin";
         }
     }
-    
-    /**
-     * Guess the MIME type of open document formats (docx and odt).
-     * It's more costly than the simple header check, but needed because open document formats
-     * are simple ZIP files on the outside and much bigger on the inside.
-     * 
-     * @param mimeType Currently detected MIME type
-     * @param file File on disk
-     * @return MIME type
-     */
-    private static String guessOpenDocumentFormat(String mimeType, Path file) {
-        if (!MimeType.APPLICATION_ZIP.equals(mimeType)) {
-            // open document formats are ZIP files
-            return mimeType;
-        }
-        
-        try (InputStream inputStream = Files.newInputStream(file);
-             ZipInputStream zipInputStream = new ZipInputStream(inputStream, Charsets.ISO_8859_1)) {
-            ZipEntry archiveEntry = zipInputStream.getNextEntry();
-            while (archiveEntry != null) {
-                if (archiveEntry.getName().equals("mimetype")) {
-                    // Maybe it's an ODT file
-                    String content = new String(IOUtils.toByteArray(zipInputStream), Charsets.ISO_8859_1);
-                    if (MimeType.OPEN_DOCUMENT_TEXT.equals(content.trim())) {
-                        mimeType = MimeType.OPEN_DOCUMENT_TEXT;
-                        break;
-                    }
-                } else if (archiveEntry.getName().equals("[Content_Types].xml")) {
-                    // Maybe it's a DOCX file
-                    String content = new String(IOUtils.toByteArray(zipInputStream), Charsets.ISO_8859_1);
-                    if (content.contains(MimeType.OFFICE_DOCUMENT)) {
-                        mimeType =  MimeType.OFFICE_DOCUMENT;
-                        break;
-                    } else if (content.contains(MimeType.OFFICE_PRESENTATION)) {
-                        mimeType = MimeType.OFFICE_PRESENTATION;
-                        break;
-                    }
-                }
-    
-                archiveEntry = zipInputStream.getNextEntry();
-            }
-        } catch (Exception e) {
-            // In case of any error, just give up and keep the ZIP MIME type
-            return mimeType;
-        }
-        
-        return mimeType;
-    }
 }

docs-core/src/main/resources/META-INF/persistence.xml

@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<persistence xmlns="http://java.sun.com/xml/ns/persistence"
+<persistence xmlns="https://jakarta.ee/xml/ns/persistence"
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+             xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
+             xsi:schemaLocation="https://jakarta.ee/xml/ns/persistence https://jakarta.ee/xml/ns/persistence/persistence_3_0.xsd"
-  version="2.0">
+             version="3.0">
   <persistence-unit name="transactions-optional" transaction-type="RESOURCE_LOCAL">
     <provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>
   </persistence-unit>

docs-core/src/main/resources/config.properties

@@ -1 +1 @@
-db.version=27
+db.version=31

docs-core/src/main/resources/db/update/dbupdate-028-0.sql

@@ -0,0 +1,2 @@
+insert into T_CONFIG(CFG_ID_C, CFG_VALUE_C) values('INBOX_STARTTLS', 'false');
+update T_CONFIG set CFG_VALUE_C = '28' where CFG_ID_C = 'DB_VERSION';

docs-core/src/main/resources/db/update/dbupdate-029-0.sql

@@ -0,0 +1,2 @@
+alter table T_FILE add column FIL_SIZE_N bigint not null default -1;
+update T_CONFIG set CFG_VALUE_C = '29' where CFG_ID_C = 'DB_VERSION';