API allows to merge files

CHANGELOG

 minerva (15.0.0~beta.2) stable; urgency=medium
+  * Improvement: API allows to merge files (#1208)
   * Small Improvement: SBO annotation support added (#1194)
   * Small Improvement: additional annotation uri qualifiers added: hasProperty,
     isPropertyOf (#1193)

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

@@ -55,6 +55,19 @@ public class ConvertController extends BaseController {
         .body(os.toByteArray());
   }
 
+  @PostMapping(value = "/merge/{fromFormat}:{toFormat}")
+  public @ResponseBody ResponseEntity<byte[]> mergeFilesToFile(
+      @PathVariable(value = "fromFormat") String fromFormat,
+      @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);
+  }
+
   @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
   public Map<String, Object> getInformation() {
     return convertController.getInformation();

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

@@ -5,6 +5,8 @@ import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
 import java.nio.charset.StandardCharsets;
 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;
@@ -15,6 +17,8 @@ import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.QueryException;
+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.*;
@@ -60,6 +64,58 @@ 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, Object> getInformation() {
     Map<String, Object> info = new LinkedHashMap<>();
 

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

 package lcsb.mapviewer.web;
 
+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.nio.file.Files;
+
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.http.MediaType;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
 
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
 @RunWith(SpringJUnit4ClassRunner.class)
 public class ConvertControllerIntegrationTest extends ControllerIntegrationTest {
 
@@ -34,4 +44,37 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
         .andExpect(status().isBadRequest());
   }
 
+  @Test
+  public void testMergeCellDesignerMaps() throws Exception {
+    byte[] body = Files.readAllBytes(new File("src/test/resources/convert/cd-maps.zip").toPath());
+    RequestBuilder request = post("/convert/merge/CellDesigner_SBML:CellDesigner_SBML")
+        .content(body);
+
+    byte[] content = mockMvc.perform(request)
+        .andExpect(status().is2xxSuccessful())
+        .andReturn().getResponse().getContentAsByteArray();
+
+    CellDesignerXmlParser parser = new CellDesignerXmlParser();
+    Model model = parser.createModel(new ConverterParams().inputStream(new ByteArrayInputStream(content)));
+
+    int s1 = 0;
+    int s2 = 0;
+    int s3 = 0;
+
+    for (Element element : model.getElements()) {
+      if (element.getName().equals("s1")) {
+        s1++;
+      }
+      if (element.getName().equals("s2")) {
+        s2++;
+      }
+      if (element.getName().equals("s3")) {
+        s3++;
+      }
+    }
+    assertEquals(1, s1);
+    assertEquals(2, s2);
+    assertEquals(1, s3);
+  }
+
 }