upload of project with invalid data overlay should fail

CHANGELOG

@@ -2,6 +2,8 @@ minerva (15.0.0~beta.3) unstable; urgency=medium
   * Improvement: API allows to merge files (#1208)
   * Bug fix: exported SBML was not compliant with the standard when element
     name was empty (#1147)
+  * Bug fix: invalid data overlays in uploaded zip file created "valid" project
+    that could not be opened (#1086)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 1 Apr 2020 14:00:00 +0200
 

service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.services.impl;
 
 import java.awt.Color;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.*;
 import java.util.Comparator;
 
@@ -151,21 +152,8 @@ public class LayoutService implements ILayoutService {
   @Override
   public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
     ColorSchemaReader reader = new ColorSchemaReader();
-    Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream());
     ColorSchemaType colorSchemaType = params.getColorSchemaType();
-    if (colorSchemaType == null) {
-      String type = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
-      if (type != null) {
-        colorSchemaType = ColorSchemaType.valueOf(type);
-      }
-    }
-    if (colorSchemaType == null) {
-      colorSchemaType = ColorSchemaType.GENERIC;
-    }
-
-    if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null && params.getColorSchemaType() != null) {
-      parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, params.getColorSchemaType().name());
-    }
+    Map<String, String> parameters = extractHeaderParameters(params.getColorInputStream(), colorSchemaType);
     final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(), parameters);
 
     // check if we can color our model using this schema,
@@ -218,6 +206,24 @@ public class LayoutService implements ILayoutService {
     return topLayout;
   }
 
+  protected Map<String, String> extractHeaderParameters(InputStream colorInputStream, ColorSchemaType colorSchemaType) throws IOException {
+    Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(colorInputStream);
+    if (colorSchemaType == null) {
+      String type = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
+      if (type != null) {
+        colorSchemaType = ColorSchemaType.valueOf(type);
+      }
+    }
+    if (colorSchemaType == null) {
+      colorSchemaType = ColorSchemaType.GENERIC;
+    }
+
+    if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null && colorSchemaType != null) {
+      parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, colorSchemaType.name());
+    }
+    return parameters;
+  }
+
   @Override
   public Layout createLayoutWithImages(final CreateLayoutParams params)
       throws IOException, InvalidColorSchemaException, CommandExecutionException {

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

@@ -50,8 +50,7 @@ import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
 import lcsb.mapviewer.services.search.chemical.IChemicalService;
 import lcsb.mapviewer.services.search.drug.IDrugService;
 import lcsb.mapviewer.services.search.mirna.IMiRNAService;
-import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.utils.EmailSender;
+import lcsb.mapviewer.services.utils.*;
 import lcsb.mapviewer.services.utils.data.BuildInLayout;
 
 /**
@@ -694,9 +693,11 @@ public class ProjectService implements IProjectService {
    *          project where the model should be placed
    * @throws InvalidInputDataExecption
    *           thrown when there is a problem with input file
+   * @throws InvalidColorSchemaException
+   * @throws IOException
    */
   protected void createModel(final CreateProjectParams params, Project dbProject)
-      throws InvalidInputDataExecption, ConverterException {
+      throws InvalidInputDataExecption, ConverterException, IOException, InvalidColorSchemaException {
     User dbUser = userDao.getById(params.getUser().getId());
     UserAnnotationSchema userAnnotationSchema = dbUser.getAnnotationSchema();
     if (userAnnotationSchema == null) {
@@ -830,7 +831,7 @@ public class ProjectService implements IProjectService {
       l.setOrderIndex(order++);
     }
     projectDao.update(project);
-
+    validateDataOverlays(project);
     if (params.isUpdateAnnotations()) {
       Map<Class<?>, List<ElementAnnotator>> annotators = null;
       if (params.getAnnotatorsMap() != null) {
@@ -853,6 +854,21 @@ public class ProjectService implements IProjectService {
 
   }
 
+  private void validateDataOverlays(final Project project) throws IOException, InvalidColorSchemaException {
+    for (Layout l : project.getLayouts()) {
+      if (l.getInputData() != null) {
+        ColorSchemaReader reader = new ColorSchemaReader();
+        Map<String, String> parameters = new LayoutService(null, null, null, null)
+            .extractHeaderParameters(new ByteArrayInputStream(l.getInputData().getFileContent()), null);
+        try {
+          reader.readColorSchema(new ByteArrayInputStream(l.getInputData().getFileContent()), parameters);
+        } catch (InvalidColorSchemaException e) {
+          throw new InvalidColorSchemaException("Problematic data overlay: " + l.getTitle() + ". " + e.getMessage(), e);
+        }
+      }
+    }
+  }
+
   private void assignZoomLevelDataToModel(Model topModel) throws InvalidInputDataExecption {
     Integer maxZoomLevels = Integer
         .parseInt(configurationService.getValue(ConfigurationElementType.MAX_NUMBER_OF_MAP_LEVELS).getValue());

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

 package lcsb.mapviewer.web;
 
+import static org.junit.Assert.assertEquals;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
@@ -20,8 +21,11 @@ import org.springframework.http.MediaType;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
 
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectStatus;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IProjectService;
 import lcsb.mapviewer.services.interfaces.IUserService;
 
 @RunWith(SpringJUnit4ClassRunner.class)
@@ -36,6 +40,9 @@ public class ProjectControllerIntegrationTestWithoutTransaction extends Controll
   @Autowired
   private IUserService userService;
 
+  @Autowired
+  private IProjectService projectService;
+
   @Before
   public void setup() {
   }
@@ -327,4 +334,60 @@ public class ProjectControllerIntegrationTestWithoutTransaction extends Controll
     }
   }
 
+  @Test
+  public void addComplexProjectWithInvalidOverlay() throws Exception {
+    User admin = userService.getUserByLogin(BUILT_IN_ADMIN_LOGIN);
+    UploadedFileEntry fileEntry = createFileInSeparateThread(
+        Files.readAllBytes(Paths.get("./src/test/resources/complex_model_with_invalid_layouts.zip")), admin);
+    try {
+      String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+          new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+          new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+          new BasicNameValuePair("parser", "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"),
+
+          new BasicNameValuePair("zip-entries[0][_type]", "MAP"),
+          new BasicNameValuePair("zip-entries[0][_filename]", "main.xml"),
+          new BasicNameValuePair("zip-entries[0][_data][root]", "true"),
+          new BasicNameValuePair("zip-entries[0][_data][name]", "s1"),
+          new BasicNameValuePair("zip-entries[0][_data][type][id]", "UNKNOWN"),
+          new BasicNameValuePair("zip-entries[0][_data][type][name]", "Unknown"),
+
+          new BasicNameValuePair("zip-entries[1][_type]", "OVERLAY"),
+          new BasicNameValuePair("zip-entries[1][_filename]", "layouts/badSchema.txt"),
+          new BasicNameValuePair("zip-entries[1][_data][name]", "test-o")
+
+      )));
+
+      RequestBuilder request = post("/projects/" + TEST_PROJECT)
+          .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+          .content(body)
+          .session(createSession(BUILT_IN_ADMIN_LOGIN, BUILT_IN_ADMIN_PASSWORD));
+
+      mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+      callInSeparateThread(() -> {
+        try {
+          waitForProjectToFinishLoading(TEST_PROJECT);
+        } catch (InterruptedException e) {
+          e.printStackTrace();
+        }
+        return null;
+      });
+
+      Project project = projectService.getProjectByProjectId(TEST_PROJECT);
+      assertEquals(ProjectStatus.FAIL, project.getStatus());
+
+    } finally {
+      callInSeparateThread(() -> {
+        try {
+          waitForProjectToFinishLoading(TEST_PROJECT);
+        } catch (InterruptedException e) {
+          e.printStackTrace();
+        }
+        return null;
+      });
+
+      removeProjectInSeparateThread(TEST_PROJECT);
+    }
+  }
+
 }