files with BOM were not processed properly

CHANGELOG

@@ -4,6 +4,7 @@ minerva (15.0.0~beta.5) unstable; urgency=medium
     (#1262)
   * Bug fix: there is a bug in PathVisio that breaks short segments being the
     end of catalist therefore short segments are removed from export (#1263) 
+  * Bug fix: conversion of file containing BOM did not work (#1264)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 2 Jun 2020 16:00:00 +0200
 

rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java

@@ -35,7 +35,7 @@ public class ConvertController extends BaseController {
   @PostMapping(value = "/{fromFormat}:{toFormat}", produces = MediaType.APPLICATION_XML_VALUE)
   public String convertInput(@PathVariable(value = "fromFormat") String fromFormat,
       @PathVariable(value = "toFormat") String toFormat,
-      @RequestBody String body)
+      @RequestBody byte[] body)
       throws IOException, QueryException, SBMLException,
       InvalidInputDataExecption, InconsistentModelException, ConverterException {
     return convertController.convert(fromFormat, toFormat, body);
@@ -45,7 +45,7 @@ public class ConvertController extends BaseController {
   public @ResponseBody ResponseEntity<byte[]> convertInputToImage(
       @PathVariable(value = "fromFormat") String fromFormat,
       @PathVariable(value = "toFormat") String toFormat,
-      @RequestBody String body)
+      @RequestBody byte[] body)
       throws IOException, QueryException, SBMLException, InvalidInputDataExecption, ConverterException,
       DrawingException {
     ByteArrayOutputStream os = convertController.converToImage(fromFormat, toFormat, body);

rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java

@@ -35,7 +35,7 @@ public class ConvertRestImpl extends BaseRestImpl {
 
   private Logger logger = LogManager.getLogger(ConvertRestImpl.class);
 
-  public String convert(String fromFormat, String toFormat, String input)
+  public String convert(String fromFormat, String toFormat, byte[] input)
       throws InvalidInputDataExecption, SBMLException, InconsistentModelException, IOException, ConverterException,
       QueryException {
     ConverterParams params = createConvertParams(input);
@@ -57,7 +57,7 @@ public class ConvertRestImpl extends BaseRestImpl {
     return IOUtils.toString(exporter.model2InputStream(model), StandardCharsets.UTF_8);
   }
 
-  public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, String input,
+  public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, byte[] input,
       Double targetWidth, Double targetHeight)
       throws InvalidInputDataExecption, SBMLException, IOException, ConverterException, DrawingException,
       QueryException {
@@ -69,7 +69,7 @@ public class ConvertRestImpl extends BaseRestImpl {
     return os;
   }
 
-  public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, String input)
+  public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, byte[] input)
       throws IOException, DrawingException, QueryException {
     try {
       return converToImage(fromFormat, toFormat, input, 0.0, 0.0);
@@ -246,9 +246,9 @@ public class ConvertRestImpl extends BaseRestImpl {
 
   }
 
-  private ConverterParams createConvertParams(String input) {
+  private ConverterParams createConvertParams(byte[] input) {
     ConverterParams params = new ConverterParams();
-    InputStream is = new ByteArrayInputStream(input.getBytes());
+    InputStream is = new ByteArrayInputStream(input);
 
     params.inputStream(is);
 

web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java

@@ -4,10 +4,11 @@ import static org.junit.Assert.assertEquals;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
-import java.io.ByteArrayInputStream;
-import java.io.File;
+import java.io.*;
 import java.nio.file.Files;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.http.MediaType;
@@ -22,6 +23,8 @@ import lcsb.mapviewer.model.map.species.Element;
 @RunWith(SpringJUnit4ClassRunner.class)
 public class ConvertControllerIntegrationTest extends ControllerIntegrationTest {
 
+  Logger logger = LogManager.getLogger();
+
   @Test
   public void testConvertInvalidFile() throws Exception {
     String body = "invalid content";
@@ -33,6 +36,23 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
         .andExpect(status().isBadRequest());
   }
 
+  @Test
+  public void convertWithBOM() throws Exception {
+    FileReader fr = new FileReader(new File("src/test/resources/SBGN_with_BOM.sbgn"));
+    BufferedReader br = new BufferedReader(fr);
+    StringBuilder tmp = new StringBuilder();
+    String line;
+    while ((line = br.readLine()) != null) {
+      tmp.append(line + System.getProperty("line.separator"));
+    }
+    RequestBuilder request = post("/convert/image/SBGN-ML:svg")
+        .content(tmp.toString().getBytes("UTF-8")).characterEncoding("UTF-8");
+
+    br.close();
+    mockMvc.perform(request)
+        .andExpect(status().is2xxSuccessful());
+  }
+
   @Test
   public void testConvertInvalidMapFormat() throws Exception {
     String body = "invalid content";

web/src/test/resources/SBGN_with_BOM.sbgn

+<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="process description">
+    <glyph id="nwtN_74c3dbfb-02b1-4e28-9d43-0cae011acf2a" class="simple chemical">
+      <label text="el2"/>
+      <bbox x="866.8349084372152" y="296.1973717584831" w="136.82486912403263" h="73.70108282346791"/>
+    </glyph>
+    <glyph id="nwtN_dea3dbde-02e4-40f9-8c27-963282d20de2" class="process">
+      <bbox x="1126.3443211534611" y="311.68061284687263" w="34.22866874880496" h="34.22866874880496"/>
+      <port id="nwtN_dea3dbde-02e4-40f9-8c27-963282d20de2.1" x="1119.4985874037002" y="328.7949472212751"/>
+      <port id="nwtN_dea3dbde-02e4-40f9-8c27-963282d20de2.2" x="1167.418723652027" y="328.7949472212751"/>
+    </glyph>
+    <glyph id="nwtN_ffaa36d2-067e-4eaa-81b0-8bf83d7e8e81" class="macromolecule">
+      <label text="el1"/>
+      <bbox x="1335.0238493448692" y="304.694418205774" w="117.05419146397195" h="78.55675869274216"/>
+    </glyph>
+    <glyph id="nwtN_c9c80149-ba98-44fe-a40c-e2ebb098d21a" class="omitted process">
+      <bbox x="1132.2447485580458" y="207.098961267922" w="39.43117860874146" h="39.43117860874146"/>
+      <port id="nwtN_c9c80149-ba98-44fe-a40c-e2ebb098d21a.1" x="1124.3585128362975" y="226.81455057229272"/>
+      <port id="nwtN_c9c80149-ba98-44fe-a40c-e2ebb098d21a.2" x="1179.5621628885356" y="226.81455057229272"/>
+    </glyph>
+    <arc id="nwtE_bce73d75-967b-4473-9028-bfc10d8af4eb" class="consumption" source="nwtN_74c3dbfb-02b1-4e28-9d43-0cae011acf2a" target="nwtN_dea3dbde-02e4-40f9-8c27-963282d20de2.1">
+      <start x="1004.2359525482459" y="331.6387380215975"/>
+      <end x="1118.8735874037002" y="328.7949472212751"/>
+    </arc>
+    <arc id="nwtE_d0911b94-b9b8-4115-b475-4d43894de402" class="production" source="nwtN_dea3dbde-02e4-40f9-8c27-963282d20de2.2" target="nwtN_ffaa36d2-067e-4eaa-81b0-8bf83d7e8e81">
+      <start x="1168.043723652027" y="328.7949472212751"/>
+      <end x="1331.2795884250613" y="340.1936113450629"/>
+    </arc>
+  </map>
+</sbgn>
\ No newline at end of file