Adds several improvements in the resources handling

- Added explicit setting of the ``UTF-8`` for the IO operations with
streams. There are some utility libraries, which are using different
default charset, which may lead to errors or unexpected behavior.
- Added explicit resource closing for all streams that we process in
some way. There were few places, where the streams were not properly
closed, which may cause memory leaks and OOM exception.
- Introduced additional return types for the result of RDF exports. Now
the result can be returned as ``File``, ``Stream`` or ``String``. This
will allow to avoid OOM exception, while buffering large data as String,
which was the previous behavior. The user may control the return type by
providing additional setting to the ``ResultFormat``, when building the
command.
- Prepared the library for the patch release ``1.6.2``.

CHANGELOG.md

@@ -1,13 +1,26 @@
 # Ontotext OntoRefine Client Library
 
-## Version 1.7
+## Version 1.6.2
 
 ### New
 
+ - Introduced additional return types for the SPARQL based RDF export. Previously the result was returned only as ``String``. There are cases, where the produced RDF
+   is quite large and if there is no enough memory to for buffering, the command throws OOM exception, while consuming the stream. With the additional types the users
+   can avoid that problem by writing the stream in the file or directly consuming it from the response object.
+   The return types are also applied for the default command for RDF export, which uses the mapping JSON from the generated from the Mapping UI.
+   The users can control the return type by providing different ``ResultType`` to the ``ResultFormat#as(ResultType)``. The default is ``STRING`` to keep the
+   library compatible and to ease the migration effort.
+
 ### Changes
 
+ - All stream IO operations are now done in ``UTF-8``. There are some utility libraries that have different default charset. To keep the library consistent and
+   the behavior predictable, we explicitly set the charset to ``UTF-8``.
+
 ### Bug fixes
 
+ - There were places, where some of the streams were not closed properly, which may cause memory leaks in specific cases. To ensure that the resources are handled
+   correctly, we've updated the logic to explicitly close all of the streams that we touch.
+
 
 ## Version 1.6.1
 

README.md

@@ -23,7 +23,7 @@ complete given operation.
  <dependency>
      <groupId>com.ontotext</groupId>
      <artifactId>ontorefine-client</artifactId>
-     <version>1.6.1</version>
+     <version>1.6.2</version>
  </dependency>
 ```
 

pom.xml

@@ -7,7 +7,7 @@
 
     <groupId>com.ontotext</groupId>
     <artifactId>ontorefine-client</artifactId>
-    <version>1.7.0-SNAPSHOT</version>
+    <version>1.6.2</version>
 
     <name>${project.groupId}:${project.artifactId}</name>
     <description>An OntoRefine Client Library</description>

src/main/java/com/ontotext/refine/client/command/ExpressionPreviewCommand.java

@@ -2,6 +2,7 @@
 
 import static com.ontotext.refine.client.util.HttpParser.HTTP_PARSER;
 import static com.ontotext.refine.client.util.JsonParser.JSON_PARSER;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.apache.commons.lang3.Validate.notBlank;
 import static org.apache.commons.lang3.Validate.notNull;
 import static org.apache.http.HttpHeaders.ACCEPT;
@@ -16,7 +17,6 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.StringJoiner;
-import org.apache.http.Consts;
 import org.apache.http.HttpResponse;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.entity.UrlEncodedFormEntity;
@@ -25,7 +25,6 @@
 import org.apache.http.message.BasicNameValuePair;
 import org.apache.http.util.EntityUtils;
 
-
 /**
  * A command to preview expressions on a project.
  */
@@ -82,7 +81,8 @@ public ExpressionPreviewResponse execute(RefineClient client) throws RefineExcep
           .post(client.createUri(endpoint()))
           .addParameter(Constants.CSRF_TOKEN, token)
           .setHeader(ACCEPT, APPLICATION_JSON.getMimeType())
-          .setEntity(new UrlEncodedFormEntity(form, Consts.UTF_8))
+          .setEntity(new UrlEncodedFormEntity(form,
+              UTF_8))
           .build();
 
       return client.execute(request, this);
@@ -97,7 +97,7 @@ public ExpressionPreviewResponse execute(RefineClient client) throws RefineExcep
   @Override
   public ExpressionPreviewResponse handleResponse(HttpResponse response) throws IOException {
     HTTP_PARSER.assureStatusCode(response, SC_OK);
-    String responseBody = EntityUtils.toString(response.getEntity());
+    String responseBody = EntityUtils.toString(response.getEntity(), UTF_8);
     return parseExpressionPreviewResponse(responseBody);
   }
 

src/main/java/com/ontotext/refine/client/command/GetProjectMetadataCommand.java

@@ -2,6 +2,7 @@
 
 import static com.ontotext.refine.client.util.HttpParser.HTTP_PARSER;
 import static com.ontotext.refine.client.util.JsonParser.JSON_PARSER;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.apache.commons.lang3.Validate.notBlank;
 import static org.apache.http.HttpHeaders.ACCEPT;
 import static org.apache.http.HttpStatus.SC_OK;
@@ -17,7 +18,6 @@
 import org.apache.http.message.BasicNameValuePair;
 import org.apache.http.util.EntityUtils;
 
-
 /**
  * A command to retrieve project meta data.
  */
@@ -52,7 +52,7 @@ public GetProjectMetadataResponse execute(RefineClient client) throws RefineExce
   @Override
   public GetProjectMetadataResponse handleResponse(HttpResponse response) throws IOException {
     HTTP_PARSER.assureStatusCode(response, SC_OK);
-    String responseBody = EntityUtils.toString(response.getEntity());
+    String responseBody = EntityUtils.toString(response.getEntity(), UTF_8);
     return new GetProjectMetadataResponse(JSON_PARSER.read(responseBody, ProjectMetadata.class));
   }
 

src/main/java/com/ontotext/refine/client/command/csrf/GetCsrfTokenCommand.java

@@ -2,6 +2,7 @@
 
 import static com.ontotext.refine.client.util.HttpParser.HTTP_PARSER;
 import static com.ontotext.refine.client.util.JsonParser.JSON_PARSER;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.apache.http.HttpHeaders.ACCEPT;
 import static org.apache.http.HttpStatus.SC_OK;
 import static org.apache.http.entity.ContentType.APPLICATION_JSON;
@@ -51,7 +52,7 @@ public GetCsrfTokenResponse execute(RefineClient client) throws RefineException
   @Override
   public GetCsrfTokenResponse handleResponse(HttpResponse response) throws IOException {
     HTTP_PARSER.assureStatusCode(response, SC_OK);
-    String responseBody = EntityUtils.toString(response.getEntity());
+    String responseBody = EntityUtils.toString(response.getEntity(), UTF_8);
     return parseGetCsrfTokenResponse(responseBody);
   }
 

src/main/java/com/ontotext/refine/client/command/delete/DeleteProjectCommand.java

@@ -2,6 +2,7 @@
 
 import static com.ontotext.refine.client.util.HttpParser.HTTP_PARSER;
 import static com.ontotext.refine.client.util.JsonParser.JSON_PARSER;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.util.Collections.singletonList;
 import static org.apache.commons.lang3.Validate.notBlank;
 import static org.apache.http.HttpHeaders.ACCEPT;
@@ -13,15 +14,13 @@
 import com.ontotext.refine.client.command.RefineCommand;
 import com.ontotext.refine.client.exceptions.RefineException;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.entity.UrlEncodedFormEntity;
 import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.client.methods.RequestBuilder;
 import org.apache.http.message.BasicNameValuePair;
 import org.apache.http.util.EntityUtils;
 
-
 /**
  * A command to delete a project.
  */
@@ -50,7 +49,7 @@ public String endpoint() {
   public DeleteProjectResponse execute(RefineClient client) throws RefineException {
     try {
       UrlEncodedFormEntity entity = new UrlEncodedFormEntity(
-          singletonList(new BasicNameValuePair("project", projectId)), StandardCharsets.UTF_8);
+          singletonList(new BasicNameValuePair("project", projectId)), UTF_8);
 
       HttpUriRequest request = RequestBuilder
           .post(client.createUri(endpoint()))
@@ -70,7 +69,7 @@ public DeleteProjectResponse execute(RefineClient client) throws RefineException
   @Override
   public DeleteProjectResponse handleResponse(HttpResponse response) throws IOException {
     HTTP_PARSER.assureStatusCode(response, SC_OK);
-    String responseBody = EntityUtils.toString(response.getEntity());
+    String responseBody = EntityUtils.toString(response.getEntity(), UTF_8);
     return parseDeleteProjectResponse(responseBody);
   }
 

src/main/java/com/ontotext/refine/client/command/models/GetProjectModelsCommand.java

@@ -6,6 +6,7 @@
 import com.ontotext.refine.client.exceptions.RefineException;
 import com.ontotext.refine.client.util.HttpParser;
 import java.io.IOException;
+import java.io.InputStream;
 import java.net.URI;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.HttpResponse;
@@ -49,8 +50,9 @@ public GetProjectModelsResponse execute(RefineClient client) throws RefineExcept
   @Override
   public GetProjectModelsResponse handleResponse(HttpResponse response) throws IOException {
     HttpParser.HTTP_PARSER.assureStatusCode(response, HttpStatus.SC_OK);
-    return new JsonMapper()
-        .readValue(response.getEntity().getContent(), GetProjectModelsResponse.class);
+    try (InputStream stream = response.getEntity().getContent()) {
+      return new JsonMapper().readValue(stream, GetProjectModelsResponse.class);
+    }
   }
 
   /**

src/main/java/com/ontotext/refine/client/command/operations/ApplyOperationsCommand.java

@@ -2,6 +2,7 @@
 
 import static com.ontotext.refine.client.util.HttpParser.HTTP_PARSER;
 import static com.ontotext.refine.client.util.JsonParser.JSON_PARSER;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.apache.commons.lang3.StringUtils.appendIfMissing;
 import static org.apache.commons.lang3.StringUtils.prependIfMissing;
 import static org.apache.commons.lang3.Validate.noNullElements;
@@ -23,7 +24,6 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.stream.Collectors;
-import org.apache.http.Consts;
 import org.apache.http.HttpResponse;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.entity.UrlEncodedFormEntity;
@@ -75,7 +75,7 @@ public ApplyOperationsResponse execute(RefineClient client) throws RefineExcepti
       String opsAsJsonArray = appendIfMissing(prependIfMissing(ops, "["), "]");
       form.add(new BasicNameValuePair("operations", opsAsJsonArray));
 
-      UrlEncodedFormEntity entity = new UrlEncodedFormEntity(form, Consts.UTF_8);
+      UrlEncodedFormEntity entity = new UrlEncodedFormEntity(form, UTF_8);
 
       HttpUriRequest request = RequestBuilder
           .post(client.createUri(endpoint()))
@@ -97,7 +97,7 @@ public ApplyOperationsResponse execute(RefineClient client) throws RefineExcepti
   @Override
   public ApplyOperationsResponse handleResponse(HttpResponse response) throws IOException {
     HTTP_PARSER.assureStatusCode(response, SC_OK);
-    String responseBody = EntityUtils.toString(response.getEntity());
+    String responseBody = EntityUtils.toString(response.getEntity(), UTF_8);
     return parseApplyOperationsResponse(responseBody);
   }
 

src/main/java/com/ontotext/refine/client/command/operations/GetOperationsCommand.java

@@ -9,14 +9,14 @@
 import com.ontotext.refine.client.exceptions.RefineException;
 import com.ontotext.refine.client.util.HttpParser;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.List;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.HttpResponse;
 import org.apache.http.HttpStatus;
 import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.client.methods.RequestBuilder;
 
-
 /**
  * A command that retrieves the operations history for specified project.
  *
@@ -53,12 +53,14 @@ public GetOperationsResponse execute(RefineClient client) throws RefineException
   @Override
   public GetOperationsResponse handleResponse(HttpResponse response) throws IOException {
     HttpParser.HTTP_PARSER.assureStatusCode(response, HttpStatus.SC_OK);
-    JsonMapper mapper = new JsonMapper();
-    JsonNode responseJson = mapper.readTree(response.getEntity().getContent());
-    List<JsonNode> operations = responseJson.findValues("operation");
-    return new GetOperationsResponse()
-        .setContent(mapper.createArrayNode().addAll(operations))
-        .setProject(project);
+    try (InputStream stream = response.getEntity().getContent()) {
+      JsonMapper mapper = new JsonMapper();
+      JsonNode responseJson = mapper.readTree(stream);
+      List<JsonNode> operations = responseJson.findValues("operation");
+      return new GetOperationsResponse()
+          .setContent(mapper.createArrayNode().addAll(operations))
+          .setProject(project);
+    }
   }
 
   /**

src/main/java/com/ontotext/refine/client/command/preferences/GetPreferenceCommand.java

@@ -8,13 +8,13 @@
 import com.ontotext.refine.client.command.RefineCommand;
 import com.ontotext.refine.client.exceptions.RefineException;
 import java.io.IOException;
+import java.io.InputStream;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.HttpResponse;
 import org.apache.http.HttpStatus;
 import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.client.methods.RequestBuilder;
 
-
 /**
  * A command to retrieve the preference for specific property.
  *
@@ -50,8 +50,10 @@ public GetPreferenceCommandResponse execute(RefineClient client) throws RefineEx
   @Override
   public GetPreferenceCommandResponse handleResponse(HttpResponse response) throws IOException {
     HTTP_PARSER.assureStatusCode(response, HttpStatus.SC_OK);
-    JsonNode json = JSON_PARSER.parseJson(response.getEntity().getContent());
-    return new GetPreferenceCommandResponse(json);
+    try (InputStream stream = response.getEntity().getContent()) {
+      JsonNode json = JSON_PARSER.parseJson(stream);
+      return new GetPreferenceCommandResponse(json);
+    }
   }
 
   /**

src/main/java/com/ontotext/refine/client/command/preferences/SetPreferenceCommand.java

@@ -2,13 +2,14 @@
 
 import static com.ontotext.refine.client.util.HttpParser.HTTP_PARSER;
 import static com.ontotext.refine.client.util.JsonParser.JSON_PARSER;
+import static java.nio.charset.StandardCharsets.UTF_8;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.ontotext.refine.client.RefineClient;
 import com.ontotext.refine.client.command.RefineCommand;
 import com.ontotext.refine.client.exceptions.RefineException;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
+import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.List;
 import org.apache.commons.lang3.Validate;
@@ -20,7 +21,6 @@
 import org.apache.http.client.methods.RequestBuilder;
 import org.apache.http.message.BasicNameValuePair;
 
-
 /**
  * A command to set preference for specific property.
  *
@@ -53,7 +53,7 @@ public SetPreferenceCommandResponse execute(RefineClient client) throws RefineEx
       HttpUriRequest request = RequestBuilder
           .post(client.createUri(endpoint()))
           .addParameter("name", property)
-          .setEntity(new UrlEncodedFormEntity(form, StandardCharsets.UTF_8))
+          .setEntity(new UrlEncodedFormEntity(form, UTF_8))
           .build();
 
       return client.execute(request, this);
@@ -70,18 +70,20 @@ public SetPreferenceCommandResponse execute(RefineClient client) throws RefineEx
   @Override
   public SetPreferenceCommandResponse handleResponse(HttpResponse response) throws IOException {
     HTTP_PARSER.assureStatusCode(response, HttpStatus.SC_OK);
-    JsonNode node = JSON_PARSER.parseJson(response.getEntity().getContent());
-    String code = JSON_PARSER.findExistingPath(node, "code").asText();
-    switch (code) {
-      case "ok":
-        return SetPreferenceCommandResponse.ok();
-      case "error":
-        String message = JSON_PARSER.findExistingPath(node, "message").asText();
-        return SetPreferenceCommandResponse.error(message);
-      default:
-        throw new RefineException(
-            "Failed to parse the response from the set preference operation for property: %s",
-            property);
+    try (InputStream stream = response.getEntity().getContent()) {
+      JsonNode node = JSON_PARSER.parseJson(stream);
+      String code = JSON_PARSER.findExistingPath(node, "code").asText();
+      switch (code) {
+        case "ok":
+          return SetPreferenceCommandResponse.ok();
+        case "error":
+          String message = JSON_PARSER.findExistingPath(node, "message").asText();
+          return SetPreferenceCommandResponse.error(message);
+        default:
+          throw new RefineException(
+              "Failed to parse the response from the set preference operation for property: %s",
+              property);
+      }
     }
   }
 

src/main/java/com/ontotext/refine/client/command/processes/GetProcessesCommand.java

@@ -11,14 +11,14 @@
 import com.ontotext.refine.client.util.HttpParser;
 import com.ontotext.refine.client.util.JsonParser;
 import java.io.IOException;
+import java.io.InputStream;
 import java.net.URI;
 import java.util.Collection;
 import org.apache.http.HttpResponse;
 import org.apache.http.HttpStatus;
 import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.client.methods.RequestBuilder;
 
-
 /**
  * A command for retrieving the processes that are currently running for project.
  *
@@ -27,7 +27,7 @@
 public class GetProcessesCommand implements RefineCommand<GetProcessesCommandResponse> {
 
   private static final TypeReference<Collection<ProjectProcess>> PROCESSES_TYPE =
-      new TypeReference<Collection<ProjectProcess>>() {};
+      new TypeReference<>() {};
 
   private final String project;
 
@@ -60,10 +60,12 @@ public GetProcessesCommandResponse execute(RefineClient client) throws RefineExc
   @Override
   public GetProcessesCommandResponse handleResponse(HttpResponse response) throws IOException {
     HttpParser.HTTP_PARSER.assureStatusCode(response, HttpStatus.SC_OK);
-    JsonNode json = JsonParser.JSON_PARSER.parseJson(response.getEntity().getContent());
-    Collection<ProjectProcess> processes =
-        JsonParser.JSON_PARSER.read(json.findValue("processes").toString(), PROCESSES_TYPE);
-    return new GetProcessesCommandResponse(processes);
+    try (InputStream stream = response.getEntity().getContent()) {
+      JsonNode json = JsonParser.JSON_PARSER.parseJson(stream);
+      Collection<ProjectProcess> processes =
+          JsonParser.JSON_PARSER.read(json.findValue("processes").toString(), PROCESSES_TYPE);
+      return new GetProcessesCommandResponse(processes);
+    }
   }
 
   /**