ConverterConvtroller separated from service

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

@@ -4,8 +4,9 @@ import java.io.*;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
 import java.nio.charset.StandardCharsets;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.logging.log4j.LogManager;
@@ -18,6 +19,7 @@ import org.springframework.web.bind.annotation.*;
 
 import lcsb.mapviewer.api.BaseController;
 import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.commands.MergeCommand;
 import lcsb.mapviewer.common.MinervaLoggerAppender;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -36,12 +38,10 @@ public class ConvertController extends BaseController {
 
   private Logger logger = LogManager.getLogger();
 
-  private ConvertRestImpl convertController;
   private List<Converter> modelConverters;
 
   @Autowired
-  public ConvertController(ConvertRestImpl convertController, List<Converter> modelConverters) {
-    this.convertController = convertController;
+  public ConvertController(List<Converter> modelConverters) {
     this.modelConverters = modelConverters;
   }
 
@@ -163,21 +163,101 @@ public class ConvertController extends BaseController {
       @PathVariable(value = "toFormat") String toFormat,
       @RequestBody byte[] body)
       throws Exception {
-    byte[] bytea = convertController.mergeFiles(fromFormat, toFormat, body);
-    return ResponseEntity.ok().contentLength(bytea.length)
-        .contentType(MediaType.APPLICATION_OCTET_STREAM)
-        .header("Content-Disposition", "attachment; filename=model" + toFormat)
-        .body(bytea);
+    try {
+      ZipInputStream zis = new ZipInputStream(new ByteArrayInputStream(body));
+      ZipEntry zipEntry = zis.getNextEntry();
+      List<Pair<String, Model>> modelsWithFilename = new ArrayList<>();
+      while (zipEntry != null) {
+        String filename = zipEntry.getName();
+        if (!zipEntry.isDirectory() && filename.toLowerCase().startsWith("maps/")) {
+
+          Model model = getModelParserByNameOrClass(fromFormat)
+              .createModel(new ConverterParams().inputStream(convertZipInputStreamToInputStream(zis, zipEntry, "UTF-8"),
+                  filename));
+          modelsWithFilename.add(new Pair<>(filename, model));
+        }
+        zipEntry = zis.getNextEntry();
+      }
+      zis.closeEntry();
+      zis.close();
+
+      modelsWithFilename.sort(new Comparator<Pair<String, Model>>() {
+
+        @Override
+        public int compare(Pair<String, Model> o1, Pair<String, Model> o2) {
+          return o1.getLeft().compareTo(o2.getLeft());
+        }
+      });
+      List<Model> models = new ArrayList<>();
+      for (Pair<String, Model> pair : modelsWithFilename) {
+        models.add(pair.getRight());
+      }
+      Model result = new MergeCommand(models).execute();
+
+      Converter exporter = getModelParserByNameOrClass(toFormat);
+      byte[] bytea = IOUtils.toByteArray(exporter.model2InputStream(result));
+      return ResponseEntity.ok().contentLength(bytea.length)
+          .contentType(MediaType.APPLICATION_OCTET_STREAM)
+          .header("Content-Disposition", "attachment; filename=model" + toFormat)
+          .body(bytea);
+    } catch (InvalidInputDataExecption | ConverterException | InconsistentModelException e) {
+      throw new QueryException("Input file is invalid", e);
+    }
+  }
+
+  private InputStream convertZipInputStreamToInputStream(ZipInputStream in, ZipEntry entry, String encoding)
+      throws IOException {
+    final int BUFFER = 2048;
+    int count = 0;
+    byte data[] = new byte[BUFFER];
+    ByteArrayOutputStream out = new ByteArrayOutputStream();
+    while ((count = in.read(data)) != -1) {
+      out.write(data, 0, count);
+    }
+    return new ByteArrayInputStream(out.toByteArray());
   }
 
   @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
-  public Map<String, ?> getInformation() {
-    return convertController.getInformation();
+  public Map<String, List<Map<String, List<String>>>> getInformation() {
+    Map<String, List<Map<String, List<String>>>> info = new LinkedHashMap<>();
+
+    List<Map<String, List<String>>> converters = new ArrayList<>();
+    for (Converter converter : modelConverters) {
+
+      List<String> names = new ArrayList<>();
+      names.add(removeWhiteSpaces(converter.getCommonName()));
+      names.add(converter.getClass().getCanonicalName());
+
+      Map<String, List<String>> names_item = new LinkedHashMap<>();
+      names_item.put("available_names", names);
+      converters.add(names_item);
+    }
+
+    info.put("inputs", converters);
+    info.put("outputs", converters);
+    return info;
   }
 
   @RequestMapping(value = "/image/", method = { RequestMethod.GET, RequestMethod.POST })
   public Map<String, ?> getInformationImage() {
-    return convertController.getInformationImage();
+    Map<String, List<Map<String, List<String>>>> info = getInformation();
+
+    List<Map<String, List<String>>> generators = new ArrayList<>();
+    ImageGenerators igs = new ImageGenerators();
+    for (Pair<String, Class<? extends AbstractImageGenerator>> generator : igs.getAvailableImageGenerators()) {
+
+      List<String> names = new ArrayList<>();
+      names.add(igs.getExtension(generator.getRight()));
+      names.add(generator.getRight().getCanonicalName());
+
+      Map<String, List<String>> names_item = new LinkedHashMap<>();
+      names_item.put("available_names", names);
+      generators.add(names_item);
+    }
+
+    info.remove("outputs");
+    info.put("outputs", generators);
+    return info;
   }
 
   private ConverterParams createConvertParams(byte[] input) {

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

-package lcsb.mapviewer.api.convert;
-
-import java.io.*;
-import java.util.*;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
-import org.apache.commons.io.IOUtils;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.MergeCommand;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.*;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.QueryException;
-
-@Transactional
-@Service
-public class ConvertRestImpl extends BaseRestImpl {
-
-  public byte[] mergeFiles(String fromFormat, String toFormat, byte[] input)
-      throws IOException, QueryException, CommandExecutionException {
-    try {
-      ZipInputStream zis = new ZipInputStream(new ByteArrayInputStream(input));
-      ZipEntry zipEntry = zis.getNextEntry();
-      List<Pair<String, Model>> modelsWithFilename = new ArrayList<>();
-      while (zipEntry != null) {
-        String filename = zipEntry.getName();
-        if (!zipEntry.isDirectory() && filename.toLowerCase().startsWith("maps/")) {
-
-          Model model = getModelParserByNameOrClass(fromFormat)
-              .createModel(new ConverterParams().inputStream(convertZipInputStreamToInputStream(zis, zipEntry, "UTF-8"),
-                  filename));
-          modelsWithFilename.add(new Pair<>(filename, model));
-        }
-        zipEntry = zis.getNextEntry();
-      }
-      zis.closeEntry();
-      zis.close();
-
-      modelsWithFilename.sort(new Comparator<Pair<String, Model>>() {
-
-        @Override
-        public int compare(Pair<String, Model> o1, Pair<String, Model> o2) {
-          return o1.getLeft().compareTo(o2.getLeft());
-        }
-      });
-      List<Model> models = new ArrayList<>();
-      for (Pair<String, Model> pair : modelsWithFilename) {
-        models.add(pair.getRight());
-      }
-      Model result = new MergeCommand(models).execute();
-
-      Converter exporter = getModelParserByNameOrClass(toFormat);
-      return IOUtils.toByteArray(exporter.model2InputStream(result));
-    } catch (InvalidInputDataExecption | ConverterException | InconsistentModelException e) {
-      throw new QueryException("Input file is invalid", e);
-    }
-  }
-
-  private InputStream convertZipInputStreamToInputStream(ZipInputStream in, ZipEntry entry, String encoding)
-      throws IOException {
-    final int BUFFER = 2048;
-    int count = 0;
-    byte data[] = new byte[BUFFER];
-    ByteArrayOutputStream out = new ByteArrayOutputStream();
-    while ((count = in.read(data)) != -1) {
-      out.write(data, 0, count);
-    }
-    return new ByteArrayInputStream(out.toByteArray());
-  }
-
-  public Map<String, List<Map<String, List<String>>>> getInformation() {
-    Map<String, List<Map<String, List<String>>>> info = new LinkedHashMap<>();
-
-    List<Map<String, List<String>>> converters = new ArrayList<>();
-    for (Converter converter : getModelConverters()) {
-
-      List<String> names = new ArrayList<>();
-      names.add(removeWhiteSpaces(converter.getCommonName()));
-      names.add(converter.getClass().getCanonicalName());
-
-      Map<String, List<String>> names_item = new LinkedHashMap<>();
-      names_item.put("available_names", names);
-      converters.add(names_item);
-    }
-
-    info.put("inputs", converters);
-    info.put("outputs", converters);
-    return info;
-  }
-
-  public Map<String, List<Map<String, List<String>>>> getInformationImage() {
-    Map<String, List<Map<String, List<String>>>> info = getInformation();
-
-    List<Map<String, List<String>>> generators = new ArrayList<>();
-    ImageGenerators igs = new ImageGenerators();
-    for (Pair<String, Class<? extends AbstractImageGenerator>> generator : igs.getAvailableImageGenerators()) {
-
-      List<String> names = new ArrayList<>();
-      names.add(igs.getExtension(generator.getRight()));
-      names.add(generator.getRight().getCanonicalName());
-
-      Map<String, List<String>> names_item = new LinkedHashMap<>();
-      names_item.put("available_names", names);
-      generators.add(names_item);
-    }
-
-    info.remove("outputs");
-    info.put("outputs", generators);
-    return info;
-  }
-
-  private Converter getModelParserByNameOrClass(String id) throws QueryException {
-    try {
-      return getModelParserByName(id);
-    } catch (QueryException e) {
-      return getModelParser(id);
-    }
-  }
-
-  private String removeWhiteSpaces(String str) {
-    return str.replace(' ', '_');
-  }
-
-  private Converter getModelParserByName(String name) throws QueryException {
-    for (Converter converter : getModelConverters()) {
-      if (removeWhiteSpaces(converter.getCommonName()).equals(name)) {
-        try {
-          return converter.getClass().newInstance();
-        } catch (InstantiationException | IllegalAccessException e) {
-          throw new InvalidStateException(e);
-        }
-      }
-    }
-    throw new QueryException("Unknown parser name: " + name);
-  }
-
-}

rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java

@@ -4,7 +4,6 @@ import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
-import lcsb.mapviewer.api.convert.AllConvertTests;
 import lcsb.mapviewer.api.files.AllFileTests;
 import lcsb.mapviewer.api.genomics.AllGenomicsTests;
 import lcsb.mapviewer.api.mesh.AllMeshTests;
@@ -13,7 +12,6 @@ import lcsb.mapviewer.api.users.AllUserTests;
 
 @RunWith(Suite.class)
 @SuiteClasses({
-    AllConvertTests.class,
     AllFileTests.class,
     AllGenomicsTests.class,
     AllMeshTests.class,

rest-api/src/test/java/lcsb/mapviewer/api/convert/AllConvertTests.java

-package lcsb.mapviewer.api.convert;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ConvertRestImplTest.class })
-public class AllConvertTests {
-
-}

rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java

-package lcsb.mapviewer.api.convert;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-import java.util.Map;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.junit.*;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.api.RestTestFunctions;
-
-public class ConvertRestImplTest extends RestTestFunctions {
-
-  @Autowired
-  public ConvertRestImpl convertRestImpl;
-  @SuppressWarnings("unused")
-  private Logger logger = LogManager.getLogger();
-
-  @AfterClass
-  public static void tearDownAfterClass() throws Exception {
-  }
-
-  @Before
-  public void setUp() throws Exception {
-  }
-
-  @After
-  public void tearDown() throws Exception {
-  }
-
-  @SuppressWarnings("unchecked")
-  @Test
-  public void testGetInformation() throws Exception {
-    Map<String, ?> result = convertRestImpl.getInformationImage();
-    assertTrue(result.keySet().size() == 2);
-    assertNotNull(result.get("inputs"));
-    assertNotNull(result.get("outputs"));
-
-    List<Object> inputs = (List<Object>) result.get("inputs");
-    List<Object> outputs = (List<Object>) result.get("outputs");
-
-    assertTrue(inputs.size() > 0);
-    assertTrue(outputs.size() > 0);
-  }
-
-  @SuppressWarnings("unchecked")
-  @Test
-  public void testGetInformationImage() throws Exception {
-    Map<String, ?> result = convertRestImpl.getInformationImage();
-    assertTrue(result.keySet().size() == 2);
-    assertNotNull(result.get("inputs"));
-    assertNotNull(result.get("outputs"));
-
-    List<Object> inputs = (List<Object>) result.get("inputs");
-    List<Object> outputs = (List<Object>) result.get("outputs");
-
-    assertTrue(inputs.size() > 0);
-    assertTrue(outputs.size() > 0);
-  }
-
-}

rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java

@@ -72,9 +72,8 @@ public class UserRestImplTest extends RestTestFunctions {
 
   private Map<String, Object> deserialize(Map<String, Object> data)
       throws JsonParseException, JsonMappingException, IOException {
-    String body = new Gson().toJson(data);
     ObjectMapper mapper = new ObjectMapper();
-    ObjectNode result = mapper.readValue(body, ObjectNode.class);
+    ObjectNode result = mapper.readValue(mapper.writeValueAsString(data), ObjectNode.class);
     return mapper.convertValue(result, Map.class);
   }
 

rest-api/testFiles/convert/newt.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_f034af08-f2b3-4912-aaa8-58b4f55f43b9" class="macromolecule">
-      <label text="dffgdf"/>
-      <bbox x="707" y="292" w="60" h="30"/>
-    </glyph>
-  </map>
-</sbgn>
\ No newline at end of file

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

@@ -17,7 +17,6 @@ import java.nio.file.Files;
 import java.util.*;
 
 import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.Test;
@@ -27,10 +26,11 @@ import org.springframework.http.MediaType;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
 
+import com.fasterxml.jackson.core.JsonParseException;
 import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonMappingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import lcsb.mapviewer.api.convert.ConvertRestImpl;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.map.model.Model;
@@ -39,9 +39,6 @@ import lcsb.mapviewer.model.map.species.Element;
 @RunWith(SpringJUnit4ClassRunner.class)
 public class ConvertControllerIntegrationTest extends ControllerIntegrationTest {
 
-  @Autowired
-  private ConvertRestImpl converterRestImpl;
-
   @Autowired
   private ObjectMapper objectMapper;
 
@@ -98,9 +95,9 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
         .andDo(document("converter/merge_maps",
             pathParameters(
                 parameterWithName("inputFormat")
-                    .description("input format, available options: " + getConverters()),
+                    .description("input format, available options: " + getModelInputConverters()),
                 parameterWithName("outputFormat")
-                    .description("output format, available options: " + getConverters()))))
+                    .description("output format, available options: " + getModelOutputConverters()))))
         .andExpect(status().is2xxSuccessful())
         .andReturn().getResponse().getContentAsByteArray();
 
@@ -162,9 +159,9 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
         .andDo(document("converter/format_conversion",
             pathParameters(
                 parameterWithName("inputFormat")
-                    .description("input format, available options: " + getConverters()),
+                    .description("input format, available options: " + getModelInputConverters()),
                 parameterWithName("outputFormat")
-                    .description("output format, available options: " + getConverters()))))
+                    .description("output format, available options: " + getModelOutputConverters()))))
         .andExpect(status().is2xxSuccessful());
   }
 
@@ -203,28 +200,12 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
         .andDo(document("converter/image_conversion",
             pathParameters(
                 parameterWithName("inputFormat")
-                    .description("input format, available options: " + getConverters()),
+                    .description("input format, available options: " + getModelInputConverters()),
                 parameterWithName("outputFormat")
-                    .description("output format, available options: " + getImageConverters()))))
+                    .description("output format, available options: " + getImageOutputConverters()))))
         .andExpect(status().is2xxSuccessful());
   }
 
-  private String getConverters() {
-    List<String> converters = new ArrayList<>();
-    for (Map<String, List<String>> entry : converterRestImpl.getInformation().get("inputs")) {
-      converters.addAll(entry.get("available_names"));
-    }
-    return StringUtils.join(converters, ", ");
-  }
-
-  private String getImageConverters() {
-    List<String> converters = new ArrayList<>();
-    for (Map<String, List<String>> entry : converterRestImpl.getInformation().get("outputs")) {
-      converters.addAll(entry.get("available_names"));
-    }
-    return StringUtils.join(converters, ", ");
-  }
-
   @Test
   public void testCelDesigner2Sbml1() throws Exception {
     String content = readFile("src/test/resources/convert/sample-cd.xml");
@@ -322,8 +303,31 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
   }
 
   private List<String> getModelOutputConverters() throws Exception {
+
+    Map<String, List<Map<String, List<String>>>> data = getModelConverters();
+
+    List<String> result = new ArrayList<>();
+    for (Map<String, List<String>> entry : data.get("outputs")) {
+      result.add(entry.get("available_names").get(0));
+    }
+
+    return result;
+  }
+
+  private List<String> getModelInputConverters() throws Exception {
+
+    Map<String, List<Map<String, List<String>>>> data = getModelConverters();
+
     List<String> result = new ArrayList<>();
+    for (Map<String, List<String>> entry : data.get("inputs")) {
+      result.add(entry.get("available_names").get(0));
+    }
 
+    return result;
+  }
+
+  private Map<String, List<Map<String, List<String>>>> getModelConverters()
+      throws UnsupportedEncodingException, Exception, IOException, JsonParseException, JsonMappingException {
     RequestBuilder request = get("/api/convert/");
 
     String response = mockMvc.perform(request)
@@ -333,6 +337,13 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
     Map<String, List<Map<String, List<String>>>> data = objectMapper.readValue(response,
         new TypeReference<Map<String, List<Map<String, List<String>>>>>() {
         });
+    return data;
+  }
+
+  private List<String> getImageOutputConverters() throws Exception {
+    List<String> result = new ArrayList<>();
+
+    Map<String, List<Map<String, List<String>>>> data = getImageConverters();
 
     for (Map<String, List<String>> entry : data.get("outputs")) {
       result.add(entry.get("available_names").get(0));
@@ -341,9 +352,8 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
     return result;
   }
 
-  private List<String> getImageOutputConverters() throws Exception {
-    List<String> result = new ArrayList<>();
-
+  private Map<String, List<Map<String, List<String>>>> getImageConverters()
+      throws UnsupportedEncodingException, Exception, IOException, JsonParseException, JsonMappingException {
     RequestBuilder request = get("/api/convert/image/");
 
     String response = mockMvc.perform(request)
@@ -353,12 +363,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
     Map<String, List<Map<String, List<String>>>> data = objectMapper.readValue(response,
         new TypeReference<Map<String, List<Map<String, List<String>>>>>() {
         });
-
-    for (Map<String, List<String>> entry : data.get("outputs")) {
-      result.add(entry.get("available_names").get(0));
-    }
-
-    return result;
+    return data;
   }