Merge remote-tracking branch 'origin/master'

README.md

@@ -81,6 +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:
@@ -122,6 +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:

docs-core/pom.xml

@@ -8,7 +8,7 @@
     <version>1.12-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
-  
+
   <modelVersion>4.0.0</modelVersion>
   <artifactId>docs-core</artifactId>
   <packaging>jar</packaging>
@@ -17,10 +17,10 @@
   <dependencies>
     <!-- Persistence layer dependencies -->
     <dependency>
-      <groupId>org.hibernate</groupId>
-      <artifactId>hibernate-core-jakarta</artifactId>
+      <groupId>org.hibernate.orm</groupId>
+      <artifactId>hibernate-core</artifactId>
     </dependency>
-    
+
     <!-- Other external dependencies -->
     <dependency>
       <groupId>joda-time</groupId>
@@ -31,12 +31,12 @@
       <groupId>com.google.guava</groupId>
       <artifactId>guava</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-compress</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
@@ -46,7 +46,7 @@
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-email</artifactId>
     </dependency>
-    
+
     <dependency>
       <groupId>org.freemarker</groupId>
       <artifactId>freemarker</artifactId>
@@ -66,17 +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>
@@ -86,17 +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>
@@ -119,30 +119,35 @@
 
     <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 -->
     <dependency>
       <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>
@@ -186,14 +191,14 @@
       <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>
@@ -205,7 +210,7 @@
           <value>dev</value>
         </property>
       </activation>
-      
+
       <build>
         <resources>
           <resource>
@@ -221,7 +226,7 @@
       <id>prod</id>
     </profile>
   </profiles>
-  
+
   <build>
     <resources>
       <resource>

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

@@ -87,7 +87,7 @@ public DocumentDto getDocument(String id, PermType perm, List<String> targetIdLi
         }
 
         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 ");
@@ -121,6 +121,7 @@ public DocumentDto getDocument(String id, PermType perm, List<String> targetIdLi
         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]);

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

@@ -19,7 +19,7 @@ public class DocumentCriteria {
     /**
      * Search query.
      */
-    private String search;
+    private String simpleSearch;
 
     /**
      * Full content search query.
@@ -96,12 +96,12 @@ public void setTargetIdList(List<String> targetIdList) {
         this.targetIdList = targetIdList;
     }
 
-    public String getSearch() {
-        return search;
+    public String getSimpleSearch() {
+        return simpleSearch;
     }
 
-    public void setSearch(String search) {
-        this.search = search;
+    public void setSimpleSearch(String search) {
+        this.simpleSearch = search;
     }
 
     public String getFullSearch() {

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

@@ -62,6 +62,7 @@ public User authenticate(String username, String password) {
             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);

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

@@ -276,9 +276,8 @@ public void findByCriteria(PaginatedList<DocumentDto> paginatedList, List<String
             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())) {
-            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);
@@ -413,14 +412,14 @@ private void suggestSearchTerms(String search, List<String> suggestionList) thro
     /**
      * 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

@@ -68,7 +68,7 @@ private static <E> void executeCountQuery(PaginatedList<E> paginatedList, QueryP
     }
 
     /**
-     * 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 @@ private static <E> List<Object[]> executeResultQuery(PaginatedList<E> paginatedL
         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/util/jpa/EMF.java

@@ -26,7 +26,7 @@
 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;
 
@@ -59,7 +59,7 @@ public void onUpgrade(int oldVersion, int newVersion) throws Exception {
         }
     }
 
-    private static Map<Object, Object> getEntityManagerProperties() {
+    private static Properties getEntityManagerProperties() {
         // Use properties file if exists
         try {
             URL hibernatePropertiesUrl = EMF.class.getResource("/hibernate.properties");
@@ -79,9 +79,13 @@ private static Map<Object, Object> getEntityManagerProperties() {
         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 (Strings.isNullOrEmpty(databaseUrl)) {
@@ -92,7 +96,7 @@ private static Map<Object, Object> getEntityManagerProperties() {
             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);
@@ -103,7 +107,7 @@ private static Map<Object, Object> getEntityManagerProperties() {
         props.put("hibernate.max_fetch_depth", "5");
         props.put("hibernate.cache.use_second_level_cache", "false");
         props.put("hibernate.connection.initial_pool_size", "1");
-        props.put("hibernate.connection.pool_size", "10");
+        props.put("hibernate.connection.pool_size", databasePoolSize);
         props.put("hibernate.connection.pool_validation_interval", "5");
         return props;
     }
@@ -136,4 +140,4 @@ public static boolean isDriverPostgresql() {
     public static String getDriver() {
         return (String) properties.get("hibernate.connection.driver_class");
     }
-}
+}

docs-core/src/test/java/com/sismics/docs/BaseTransactionalTest.java

@@ -30,7 +30,7 @@
  */
 public abstract class BaseTransactionalTest extends BaseTest {
     @Before
-    public void setUp() throws Exception {
+    public void setUp() {
         // Initialize the entity manager
         EntityManager em = EMF.get().createEntityManager();
         ThreadLocalContext context = ThreadLocalContext.get();
@@ -40,7 +40,8 @@ public void setUp() throws Exception {
     }
 
     @After
-    public void tearDown() throws Exception {
+    public void tearDown() {
+        ThreadLocalContext.get().getEntityManager().getTransaction().rollback();
     }
 
     protected User createUser(String userName) throws Exception {

docs-web-common/pom.xml

@@ -68,6 +68,12 @@
       <groupId>org.slf4j</groupId>
       <artifactId>jul-to-slf4j</artifactId>
     </dependency>
+
+    <dependency>
+      <groupId>com.auth0</groupId>
+      <artifactId>java-jwt</artifactId>
+      <version>4.4.0</version>
+    </dependency>
 
     <!-- Test dependencies -->
     <dependency>

docs-web-common/src/main/java/com/sismics/rest/util/ValidationUtil.java

@@ -21,7 +21,7 @@ public class ValidationUtil {
 
     private static Pattern ALPHANUMERIC_PATTERN = Pattern.compile("[a-zA-Z0-9_]+");
 
-    private static Pattern USERNAME_PATTERN = Pattern.compile("[a-zA-Z0-9_@\\.]+");
+    private static Pattern USERNAME_PATTERN = Pattern.compile("[a-zA-Z0-9_@.-]+");
 
     /**
      * Checks that the argument is not null.