Merge branch '97-data-upload' into 'master'

Resolve "data upload"

Closes #97

See merge request !43

commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java

@@ -15,6 +15,8 @@ import java.util.Map;
  */
 public final class TextFileUtils {
 
+	public static String COLUMN_COUNT_PARAM = "__COLUMN_COUNT";
+
 	/**
 	 * Default constructor that prevents instatiation.
 	 */
@@ -46,6 +48,9 @@ public final class TextFileUtils {
 					result.put(key, value);
 				}
 			} else {
+				String key = COLUMN_COUNT_PARAM;
+				String value = line.split("\t").length + "";
+				result.put(key, value);
 				break;
 			}
 		}

frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js

@@ -8,6 +8,9 @@ var PanelControlElementType = require('../PanelControlElementType');
 var GuiConnector = require('../../GuiConnector');
 var logger = require('../../logger');
 var Functions = require('../../Functions');
+var NetworkError = require('../../NetworkError');
+
+var HttpStatus = require('http-status-codes');
 
 function OverlayPanel(params) {
   params.panelName = "overlays";
@@ -369,21 +372,22 @@ OverlayPanel.prototype.parseFile = function(fileContent) {
 OverlayPanel.prototype.openAddOverlayDialog = function() {
   var self = this;
   var fileContent = null;
+  var contentInput = null;
   var content = document.createElement("div");
   content.style.width = "100%";
   content.style.height = "100%";
-  content.appendChild(self.createLabel("Name"));
+  content.appendChild(self.createLabel("Name: "));
   var nameInput = self.createInputText();
   content.appendChild(nameInput);
   content.appendChild(self.createNewLine());
 
-  content.appendChild(self.createLabel("Description"));
+  content.appendChild(self.createLabel("Description: "));
   content.appendChild(self.createNewLine());
   var descriptionInput = self.createTextArea();
   content.appendChild(descriptionInput);
   content.appendChild(self.createNewLine());
 
-  content.appendChild(self.createLabel("File"));
+  content.appendChild(self.createLabel("Upload file: "));
   var fileInput = self.createFileButton();
   fileInput.addEventListener("change", function() {
     fileContent = null;
@@ -415,12 +419,24 @@ OverlayPanel.prototype.openAddOverlayDialog = function() {
   content.appendChild(fileInput);
   content.appendChild(self.createNewLine());
 
+  content.appendChild(self.createLabel("Or privde list of elements here: "));
+  content.appendChild(self.createNewLine());
+  contentInput = self.createTextArea();
+  content.appendChild(contentInput);
+  content.appendChild(self.createNewLine());
+
   var buttons = [ {
     text : "UPLOAD",
     click : function() {
       var dialog = this;
+      if (contentInput.value !== undefined && contentInput.value !== null) {
+        contentInput.value = contentInput.value.trim();
+        if (contentInput.value !== "") {
+          fileContent = contentInput.value;
+        }
+      }
       if (fileContent === null) {
-        GuiConnector.alert("No file was selected");
+        GuiConnector.alert("Neither file was selected nor data was enterd");
       } else {
         var data = {
           name : nameInput.value,
@@ -433,6 +449,16 @@ OverlayPanel.prototype.openAddOverlayDialog = function() {
           return self.refresh();
         }).then(function() {
           $(dialog).dialog("close");
+        }, function(error) {
+          if (error instanceof NetworkError) {
+            if (error.statusCode === HttpStatus.BAD_REQUEST) {
+              GuiConnector.alert("Problematic input: <br/>" + error.content);
+            } else {
+              throw error;
+            }
+          } else {
+            throw error;
+          }
         });
       }
     }

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

@@ -95,7 +95,11 @@ public class ColorSchemaReader {
 	 */
 	public Collection<ColorSchema> readColorSchema(InputStream colorInputStream, Map<String, String> params) throws IOException, InvalidColorSchemaException {
 		if (params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null) {
-			return readGenericColorSchema(colorInputStream);
+			if (Integer.valueOf(params.get(TextFileUtils.COLUMN_COUNT_PARAM)) == 1) {
+				return readSimpleNameColorSchema(colorInputStream);
+			} else {
+				return readGenericColorSchema(colorInputStream);
+			}
 		} else {
 			ColorSchemaType type = ColorSchemaType.valueOf(params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
 			if (type == null) {
@@ -550,6 +554,35 @@ public class ColorSchemaReader {
 		return result;
 	}
 
+	protected Collection<ColorSchema> readSimpleNameColorSchema(InputStream colorInputStream) throws IOException, InvalidColorSchemaException {
+		List<ColorSchema> result = new ArrayList<>();
+
+		BufferedReader br = new BufferedReader(new InputStreamReader(colorInputStream));
+
+		try {
+			String line = br.readLine();
+			while (line != null && line.startsWith("#")) {
+				line = br.readLine();
+			}
+
+			while (line != null) {
+				if (line.trim().equals("")) {
+					line = br.readLine();
+					continue;
+				}
+				String[] values = line.split("\t", -1);
+				ColorSchema schema = new GenericColorSchema();
+				processNameColumn(schema, values[0]);
+				schema.setValue(1.0);
+				result.add(schema);
+				line = br.readLine();
+			}
+		} finally {
+			br.close();
+		}
+		return result;
+	}
+
 	/**
 	 * Sets proper reaction identifier to {@link ColorSchema} from cell content.
 	 * 

service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java

@@ -11,6 +11,7 @@ import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Collection;
 
 import org.apache.commons.io.output.ByteArrayOutputStream;
@@ -279,4 +280,17 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
 		}
 	}
 
+	@Test
+	public void testSimpleNameSchemas() throws Exception {
+		try {
+			ColorSchemaReader reader = new ColorSchemaReader();
+			String input = "#header\ns1\ns2\n";
+			Collection<ColorSchema> schemas = reader.readSimpleNameColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
+			assertEquals(2, schemas.size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
 }

web/src/main/webapp/resources/css/global.css

@@ -137,7 +137,6 @@ table.mapInfoBoxResultsTable, table.mapInfoBoxResultsTable th, table.mapInfoBoxR
 }
 
 .searchPanel {
-	height: 100%;
 	background-color: #FFFFFF;
 	box-shadow: 0 3px 30px #B9B9B9;
 	padding: 15px;