provide info about deprecated columns in API

rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java

@@ -12,6 +12,7 @@ import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.*;
 import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.cache.FileEntry;
@@ -26,6 +27,8 @@ import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
 import lcsb.mapviewer.persist.dao.map.LayoutDao;
 import lcsb.mapviewer.services.interfaces.ILayoutService;
 import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
+import lcsb.mapviewer.services.utils.ColorSchemaReader;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
 
 @Transactional
 @Service
@@ -78,6 +81,8 @@ public class OverlayRestImpl extends BaseRestImpl {
     result.put("description", overlay.getDescription());
     result.put("publicOverlay", overlay.isPublicLayout());
     result.put("defaultOverlay", overlay.isDefaultOverlay());
+
+    result.put("deprecatedColumns", getDeprecatedColumns(overlay));
     result.put("googleLicenseConsent", overlay.isGoogleLicenseConsent());
     List<Map<String, Object>> images = new ArrayList<>();
     List<DataOverlayImageLayer> imageList = new ArrayList<>(overlay.getDataOverlayImageLayers());
@@ -97,6 +102,18 @@ public class OverlayRestImpl extends BaseRestImpl {
     return result;
   }
 
+  private String getDeprecatedColumns(Layout overlay) {
+    try {
+      String result = "";
+      for (ColorSchemaColumn column : new ColorSchemaReader().getDeprecatedColumns(overlay)) {
+        result += column.name() + ",";
+      }
+      return result;
+    } catch (IOException | InvalidColorSchemaException e) {
+      throw new InvalidStateException(e);
+    }
+  }
+
   public List<Map<String, Object>> getOverlayElements(String projectId, int overlayId, String columns)
       throws QueryException {
 

service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java

 package lcsb.mapviewer.services.utils;
 
-import java.awt.*;
+import java.awt.Color;
 import java.io.*;
 import java.lang.reflect.Field;
 import java.util.*;
-import java.util.List;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
@@ -12,8 +11,7 @@ import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.annotation.services.MiriamConnector;
 import lcsb.mapviewer.common.*;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.exception.*;
 import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
 import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
@@ -808,4 +806,32 @@ public class ColorSchemaReader {
     }
     return readColorSchema(new ByteArrayInputStream(inputData), params);
   }
+
+  public List<ColorSchemaColumn> getDeprecatedColumns(Layout overlay)
+      throws IOException, InvalidColorSchemaException {
+    List<ColorSchemaColumn> result = new ArrayList<>();
+    BufferedReader br = new BufferedReader(
+        new InputStreamReader(new ByteArrayInputStream(overlay.getInputData().getFileContent())));
+
+    String line = br.readLine();
+    while (line != null && line.startsWith("#")) {
+      line = br.readLine();
+    }
+    String[] columns = line.split("\t");
+
+    Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
+    parseColumns(columns, schemaColumns, ColorSchemaType.GENERIC);
+    for (ColorSchemaColumn column : schemaColumns.keySet()) {
+      try {
+        Field f = ColorSchemaColumn.class.getField(column.name());
+        if (column.getDepractedColumnName() != null || f.isAnnotationPresent(Deprecated.class)) {
+          result.add(column);
+        }
+      } catch (NoSuchFieldException | SecurityException e) {
+        throw new InvalidStateException(e);
+      }
+    }
+    return result;
+  }
+
 }

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

 package lcsb.mapviewer.web;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
@@ -34,6 +34,7 @@ import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.map.LayoutDao;
 import lcsb.mapviewer.services.interfaces.IModelService;
 import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @Transactional
@@ -422,9 +423,8 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
         .getAsJsonArray().size());
   }
 
-  private Layout createOverlay(User admin) {
+  private Layout createOverlay(User admin, String content) {
     UploadedFileEntry file = new UploadedFileEntry();
-    String content = "elementIdentifier\tvalue\n\t-1";
     file.setFileContent(content.getBytes());
     file.setLength(content.getBytes().length);
 
@@ -436,6 +436,10 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
     return overlay;
   }
 
+  private Layout createOverlay(User admin) {
+    return createOverlay(admin, "elementIdentifier\tvalue\n\t-1");
+  }
+
   @Test
   public void testGetReactionsForOverlay() throws Exception {
     User admin = createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
@@ -1028,4 +1032,31 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
         .andExpect(status().is2xxSuccessful());
   }
 
+  @Test
+  public void testDeprecatedOverlayInformation() throws Exception {
+    createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
+
+    Layout overlay = createOverlay(null,
+        "elementIdentifier\t" + ColorSchemaColumn.REACTION_IDENTIFIER + "\tvalue\n\t\t-1");
+    overlay.setPublicLayout(true);
+    layoutDao.update(overlay);
+
+    MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
+
+    RequestBuilder request = get(
+        "/projects/" + TEST_PROJECT + "/overlays/" + overlay.getId() + "/")
+            .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+            .session(session);
+
+    String response = mockMvc.perform(request)
+        .andExpect(status().is2xxSuccessful())
+        .andReturn().getResponse().getContentAsString();
+    String deprecatedColumns = new JsonParser()
+        .parse(response)
+        .getAsJsonObject().get("deprecatedColumns").getAsString();
+
+    assertNotNull(deprecatedColumns);
+    assertFalse(deprecatedColumns.isEmpty());
+  }
+
 }