From f84e94a29e53358a302cbf485ff4ce4a307a4ad8 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 25 Jul 2019 16:55:36 +0200
Subject: [PATCH] provide info about deprecated columns in API
---
.../projects/overlays/OverlayRestImpl.java | 17 +++++++++
.../services/utils/ColorSchemaReader.java | 34 +++++++++++++++--
.../web/OverlayControllerIntegrationTest.java | 37 +++++++++++++++++--
3 files changed, 81 insertions(+), 7 deletions(-)
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index 46a8341717..0ff7457c83 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/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 {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 72200ad594..a77487a00a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -1,10 +1,9 @@
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;
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index f0dfd1ee1f..705f1000d0 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
@@ -1,6 +1,6 @@
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());
+ }
+
}
--
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