Merge branch 'devel_12.0.x'

CHANGELOG

@@ -11,6 +11,18 @@ minerva (12.1.0~alpha.0) experimental; urgency=medium
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 25 Jul 2018 10:00:00 +0200
 
+minerva (12.0.2) stable; urgency=medium
+  * Bug fix: data overlay by annotation type fixed
+  * Bug fix: [plugin] getting reactions with set of id larger than 100 elements
+    works properly
+  * Bug fix: name of commented protein was remembered for the new comment
+  * Bug fix: setting zoom level wasn't ranged and validated
+  * Bug fix: when uploading data overlay there is a warning regarding mixed new
+    line characters when necessary
+  * Performance: tomcat inside docker image by default can use 3G of memory
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
+
 minerva (12.0.1) stable; urgency=medium
   * Bug fix: setting default zoom level on submap
   * Bug fix: opened submap had different background then current selection

Docker/Dockerfile

@@ -45,6 +45,7 @@ ADD policy-rc.d /tmp/policy-rc.d
 
 RUN apt-get update
 
+RUN sed -i "/JAVA_OPTS=\"-Djava.awt.headless=true -Xmx128m -XX:+UseConcMarkSweepGC\"/c\JAVA_OPTS=\"-Djava.awt.headless=true -Xmx3096m -XX:+UseConcMarkSweepGC\"" /etc/default/tomcat7
 
 #when we install minerva allow to start services, so everything can be installed properly
 #but we need to disable tomcat7 because tomcat7 requires SYS_PTRACE and we cannot start it:

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java

@@ -27,7 +27,6 @@ import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.species.Chemical;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.ChebiWebServiceFault_Exception;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.Entity;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.LiteEntity;
@@ -205,7 +204,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
           }
         }
       }
-    } catch (ChebiWebServiceFault_Exception e) {
+    } catch (Exception e) {
       throw new ChebiSearchException("Problem with chebi connection", e);
     }
     return null;
@@ -290,7 +289,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
       String value = miriamListToStringList(result);
 
       setCacheValue(query, value);
-    } catch (ChebiWebServiceFault_Exception e) {
+    } catch (Exception e) {
       throw new ChebiSearchException("Problem with chebi", e);
     }
     return result;
@@ -300,7 +299,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
    * Serialize list of chebi identifiers.
    * 
    * @param list
-   *          list of chebi identfiers
+   *          list of chebi identifiers
    * @return string with identifiers
    */
   private String miriamListToStringList(List<MiriamData> list) {
@@ -357,7 +356,6 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
     }
     try {
       ChebiWebServiceClient client = getClient();
-
       LiteEntityList entities = client.getLiteEntity(id, SearchCategory.CHEBI_ID, MAX_SEARCH_RESULTS_FROM_CHEBI_API,
           StarsCategory.ALL);
       List<LiteEntity> resultList = entities.getListElement();
@@ -374,7 +372,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
         setCacheValue("id: " + id, chebiSerializer.objectToString(result));
       }
       return result;
-    } catch (ChebiWebServiceFault_Exception e) {
+    } catch (Exception e) {
       throw new ChebiSearchException("Problem with chebi", e);
     }
   }
@@ -387,7 +385,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
    *          identifier): "CHEBI:XXXXX" or "XXXXX"
    * @return common name of chemical
    * @throws ChebiSearchException
-   *           thrown when there is a problemw ith accessing information from
+   *           thrown when there is a problem with accessing information from
    *           external chebi database
    */
   protected String getChebiNameForChebiId(MiriamData id) throws ChebiSearchException {

frontend-js/src/main/js/ServerConnector.js

@@ -74,6 +74,7 @@ ServerConnector.init = function () {
     self.removeListener("onDataLoadStop", listeners[i]);
   }
 
+  self.MAX_NUMBER_OF_IDS_IN_GET_QUERY = 100;
 };
 ServerConnector.registerListenerType("onDataLoadStart");
 ServerConnector.registerListenerType("onDataLoadStop");
@@ -238,10 +239,19 @@ ServerConnector._sendRequest = function (params) {
  * @returns {Promise}
  */
 ServerConnector.sendPostRequest = function (url, params) {
+  var formParams = {};
+  for (var key in params) {
+    if (params.hasOwnProperty(key)) {
+      formParams[key] = this.objectToRequestString(params[key]);
+      if (formParams[key] === undefined) {
+        formParams[key] = params[key];
+      }
+    }
+  }
   return this.sendRequest({
     method: "POST",
     url: url,
-    form: params
+    form: formParams
   });
 };
 
@@ -289,6 +299,25 @@ ServerConnector.getServerBaseUrl = function () {
   return this._serverBaseUrl;
 };
 
+/**
+ *
+ * @param {Object} object
+ * @returns {string}
+ */
+ServerConnector.objectToRequestString = function (object) {
+  var value;
+  if (object instanceof Point) {
+    value = this.pointToString(object);
+  } else if (Object.prototype.toString.call(object) === '[object Array]') {
+    value = this.idsToString(object);
+  } else if (typeof object === 'string' || object instanceof String || !isNaN(object)) {
+    value = object.toString();
+  } else {
+    value = undefined;
+  }
+  return value;
+};
+
 ServerConnector.createGetParams = function (params, prefix) {
   var sorted = [], key;
 
@@ -306,18 +335,12 @@ ServerConnector.createGetParams = function (params, prefix) {
     if (prefix !== undefined) {
       key = prefix + "." + key;
     }
-    if (value instanceof Point) {
-      value = this.pointToString(value);
-    } else if (Object.prototype.toString.call(value) === '[object Array]') {
-      value = this.idsToString(value);
-    } else if (typeof value === 'string' || value instanceof String || !isNaN(value)) {
-    } else {
-      result += this.createGetParams(value, key);
-      value = undefined;
-    }
 
-    if (value !== undefined && value !== "") {
-      result += key + "=" + value + "&";
+    var serializedValue = this.objectToRequestString(value);
+    if (serializedValue === undefined) {
+      result += this.createGetParams(value, key);
+    } else if (serializedValue !== undefined && serializedValue !== "") {
+      result += key + "=" + serializedValue + "&";
     }
   }
   return result;
@@ -1513,6 +1536,15 @@ ServerConnector.getOverlayById = function (overlayId, projectId) {
   });
 };
 
+/**
+ *
+ * @param {number} [params.modelId]
+ * @param {number[]} [params.ids]
+ * @param {number[]} [params.participantId]
+ * @param {string[]} [params.columns]
+ * @param {string} [params.projectId]
+ * @returns {*}
+ */
 ServerConnector.getReactions = function (params) {
   var self = this;
   var queryParams = {
@@ -1531,7 +1563,7 @@ ServerConnector.getReactions = function (params) {
   };
   return self.getProjectId(params.projectId).then(function (result) {
     queryParams.projectId = result;
-    if (filterParams.id.length > 100 || filterParams.participantId.length > 100) {
+    if (filterParams.id.length > self.MAX_NUMBER_OF_IDS_IN_GET_QUERY || filterParams.participantId.length > self.MAX_NUMBER_OF_IDS_IN_GET_QUERY) {
       return self.sendPostRequest(self.getReactionsUrl(queryParams), filterParams);
     } else {
       return self.sendGetRequest(self.getReactionsUrl(queryParams, filterParams));
@@ -1571,7 +1603,7 @@ ServerConnector.getAliases = function (params) {
   };
   return self.getProjectId(params.projectId).then(function (result) {
     queryParams.projectId = result;
-    if (filterParams.id.length > 100) {
+    if (filterParams.id.length > self.MAX_NUMBER_OF_IDS_IN_GET_QUERY) {
       return self.sendPostRequest(self.getAliasesUrl(queryParams), filterParams);
     } else {
       return self.sendGetRequest(self.getAliasesUrl(queryParams, filterParams));

frontend-js/src/main/js/gui/AddOverlayDialog.js

@@ -154,6 +154,10 @@ AddOverlayDialog.prototype.processFile = function (file) {
           if (overlay.getType() !== undefined) {
             typeSelect.val(overlay.getType());
           }
+          if (overlayParser.containsMixedNewLineCharacters(evt.target.result)) {
+            GuiConnector.warn("Selected file contains new line characters from different operating systems " +
+              "(MAC/Windows/Linux). This might cause confusion when reading the file in the editor later on.")
+          }
           resolve(self.getFileContent());
         } catch (error) {
           reject(error);

frontend-js/src/main/js/gui/CommentDialog.js

@@ -38,13 +38,13 @@ function createRow(elements) {
   return row;
 }
 
-CommentDialog.prototype.open = function (types) {
+CommentDialog.prototype.open = function (identifiedElements) {
   var self = this;
   self.setTypes([CommentDialog.GENERAL]);
 
   var promises = [CommentDialog.GENERAL];
-  for (var i = 0; i < types.length; i++) {
-    var ie = types[i];
+  for (var i = 0; i < identifiedElements.length; i++) {
+    var ie = identifiedElements[i];
     if (ie.getType() === "ALIAS") {
       promises.push(self.getMap().getSubmapById(ie.getModelId()).getModel().getAliasById(ie.getId(), true));
     } else if (ie.getType() === "REACTION") {
@@ -182,6 +182,7 @@ CommentDialog.prototype.setTypes = function (types) {
   typeOptions.value = 0;
 
   this._types = types;
+  typeOptions.onchange();
 };
 
 CommentDialog.prototype.getTypes = function () {

frontend-js/src/main/js/gui/admin/EditProjectDialog.js

@@ -114,7 +114,7 @@ EditProjectDialog.prototype.addTab = function (params) {
     navigationObject: navLi,
     navigationBar: params.tabMenuDiv
   });
-  $(contentDiv).css("overflow","auto");
+  $(contentDiv).css("overflow", "auto");
 
   if (params.content !== undefined) {
     contentDiv.appendChild(params.content);
@@ -821,7 +821,12 @@ function getValueOrEmpty(value) {
   }
 }
 
-EditProjectDialog.prototype.mapToTableRow = function (map, users) {
+/**
+ *
+ * @param {MapModel} map
+ * @returns {Array}
+ */
+EditProjectDialog.prototype.mapToTableRow = function (map) {
   var row = [];
   var id = map.getId();
   var centerX = getValueOrEmpty(map.getDefaultCenterX());
@@ -831,7 +836,17 @@ EditProjectDialog.prototype.mapToTableRow = function (map, users) {
   row[1] = map.getName();
   row[2] = "<input name='defaultCenterX-" + id + "' value='" + centerX + "'/>";
   row[3] = "<input name='defaultCenterY-" + id + "' value='" + centerY + "'/>";
-  row[4] = "<input name='defaultZoomLevel-" + id + "' value='" + zoomLevel + "'/>";
+  var zoomLevelSelect = "<select name='defaultZoomLevel-" + id + "' value='" + zoomLevel + "'>" +
+    "<option value=''>---</option>";
+  for (var i = map.getMinZoom(); i <= map.getMaxZoom(); i++) {
+    var selected = "";
+    if (i === zoomLevel) {
+      selected = " selected ";
+    }
+    zoomLevelSelect += "<option value='" + i + "' " + selected + ">" + (i - map.getMinZoom()) + "</option>";
+  }
+  zoomLevelSelect += "</select>";
+  row[4] = zoomLevelSelect;
   row[5] = "<button name='saveMap' data='" + id + "'><i class=\"fa fa-save\" style=\"font-size:17px\"></i></button>";
 
   return row;
@@ -921,8 +936,10 @@ EditProjectDialog.prototype.saveOverlay = function (overlayId) {
 EditProjectDialog.prototype.saveMap = function (mapId) {
   var self = this;
   var map = self._mapsById[mapId];
-  map.setDefaultCenterX($("[name='defaultCenterX-" + mapId + "']", self.getElement())[0].value);
-  map.setDefaultCenterY($("[name='defaultCenterY-" + mapId + "']", self.getElement())[0].value);
+  var centerX = parseInt($("[name='defaultCenterX-" + mapId + "']", self.getElement())[0].value);
+  var centerY = parseInt($("[name='defaultCenterY-" + mapId + "']", self.getElement())[0].value);
+  map.setDefaultCenterX(centerX);
+  map.setDefaultCenterY(centerY);
   map.setDefaultZoomLevel($("[name='defaultZoomLevel-" + mapId + "']", self.getElement())[0].value);
 
   return ServerConnector.updateModel({projectId: self.getProject().getProjectId(), model: map});

frontend-js/src/main/js/map/OverlayParser.js

@@ -9,13 +9,24 @@ function OverlayParser() {
 
 /**
  *
- * @param {string| Uint8Array|ArrayBuffer} content
- * @returns {DataOverlay}
+ * @param {string| Uint8Array | ArrayBuffer} content
+ * @returns {string}
+ * @private
  */
-OverlayParser.prototype.parse = function (content) {
+OverlayParser.prototype._extractContent = function (content) {
   if (content instanceof Uint8Array || content instanceof ArrayBuffer) {
     content = new TextDecoder("UTF8").decode(content);
   }
+  return content;
+};
+
+/**
+ *
+ * @param {string| Uint8Array|ArrayBuffer} content
+ * @returns {DataOverlay}
+ */
+OverlayParser.prototype.parse = function (content) {
+  content = this._extractContent(content);
   var data = {content: content};
   var lines = content.split("\n");
   for (var i = 0; i < lines.length; i++) {
@@ -42,5 +53,36 @@ OverlayParser.prototype.parse = function (content) {
   return new DataOverlay(data);
 };
 
+/**
+ *
+ * @param {string| Uint8Array | ArrayBuffer} content
+ * @returns {boolean}
+ */
+OverlayParser.prototype.containsMixedNewLineCharacters = function (content) {
+  content = this._extractContent(content);
+  var newLineRegEx = /[\r\n]+/g;
+  var match = newLineRegEx.exec(content);
+  var newLineFormats = {};
+  var counter = 0;
+  while (match !== null && match !== undefined) {
+    var foundMultiplication = false;
+    var key = '';
+    //this is just a heuristic - let's assume there are at most 10 empty lines in a file
+    for (var i = 0; i < 10; i++) {
+      key += match[0];
+      if (newLineFormats[key]) {
+        foundMultiplication = true;
+      } else {
+        newLineFormats[key] = true;
+      }
+    }
+    if (!foundMultiplication) {
+      counter++;
+    }
+    match = newLineRegEx.exec(content);
+  }
+  return counter > 1;
+};
+
 
 module.exports = OverlayParser;

frontend-js/src/main/js/map/data/MapModel.js

@@ -455,8 +455,16 @@ MapModel.prototype.getDefaultZoomLevel = function () {
   return this._defaultZoomLevel;
 };
 
+/**
+ *
+ * @param {number} defaultZoomLevel
+ */
 MapModel.prototype.setDefaultZoomLevel = function (defaultZoomLevel) {
-  this._defaultZoomLevel = defaultZoomLevel;
+  if (!isNaN(defaultZoomLevel)) {
+    this._defaultZoomLevel = defaultZoomLevel;
+  } else {
+    this._defaultZoomLevel = null;
+  }
 };
 
 /**
@@ -467,8 +475,16 @@ MapModel.prototype.getDefaultCenterX = function () {
   return this._defaultCenterX;
 };
 
+/**
+ *
+ * @param {number} defaultCenterX
+ */
 MapModel.prototype.setDefaultCenterX = function (defaultCenterX) {
-  this._defaultCenterX = defaultCenterX;
+  if (!isNaN(defaultCenterX)) {
+    this._defaultCenterX = defaultCenterX;
+  } else {
+    this._defaultCenterX = null;
+  }
 };
 
 /**
@@ -480,7 +496,11 @@ MapModel.prototype.getDefaultCenterY = function () {
 };
 
 MapModel.prototype.setDefaultCenterY = function (defaultCenterY) {
-  this._defaultCenterY = defaultCenterY;
+  if (!isNaN(defaultCenterY)) {
+    this._defaultCenterY = defaultCenterY;
+  } else {
+    this._defaultCenterY = null;
+  }
 };
 
 MapModel.prototype.getSubmodelType = function () {

frontend-js/src/test/js/ServerConnector-test.js

@@ -13,6 +13,7 @@ var LayoutAlias = require('../../main/js/map/data/LayoutAlias');
 var MapModel = require('../../main/js/map/data/MapModel');
 var NetworkError = require('../../main/js/NetworkError');
 var Project = require('../../main/js/map/data/Project');
+var Point = require('../../main/js/map/canvas/Point');
 var Reaction = require('../../main/js/map/data/Reaction');
 var ServerConnector = require('../../main/js/ServerConnector');
 var SecurityError = require('../../main/js/SecurityError');
@@ -110,7 +111,7 @@ describe('ServerConnector', function () {
       });
     });
     it('without ids', function () {
-      return ServerConnector.getReactions([]).then(function (result) {
+      return ServerConnector.getReactions({}).then(function (result) {
         assert.equal(result.length, 28);
         var reaction = result[0];
         assert.ok(reaction instanceof Reaction);
@@ -118,6 +119,32 @@ describe('ServerConnector', function () {
         assert.equal(reaction.getModelId(), 15781);
       });
     });
+
+    it('with ids', function () {
+      return ServerConnector.getReactions({
+        modelId: 15781,
+        participantId: [329156, 329157, 329158, 329159, 329160, 329161, 329162, 329163, 329164, 329165, 329166, 329167, 329168, 329169, 329170, 329171, 329172, 329173, 329174, 329175, 329176, 329177, 329178, 329179, 329180, 329181, 329182, 329183, 329184, 329185]
+      }).then(function (result) {
+        assert.equal(result.length, 28);
+        var reaction = result[0];
+        assert.ok(reaction instanceof Reaction);
+        assert.equal(reaction.getId(), 153524);
+        assert.equal(reaction.getModelId(), 15781);
+      });
+    });
+    it('with ids when asking for too many elements for gett query', function () {
+      ServerConnector.MAX_NUMBER_OF_IDS_IN_GET_QUERY = 0;
+      return ServerConnector.getReactions({
+        modelId: 15781,
+        participantId: [329167]
+      }).then(function (result) {
+        assert.equal(result.length, 5);
+        var reaction = result[0];
+        assert.ok(reaction instanceof Reaction);
+        assert.equal(reaction.getId(), 153518);
+        assert.equal(reaction.getModelId(), 15781);
+      });
+    });
   });
 
 
@@ -420,4 +447,23 @@ describe('ServerConnector', function () {
   });
 
 
+  describe('objectToRequestString', function () {
+    it('string', function () {
+      assert.equal("test_string", ServerConnector.objectToRequestString("test_string"));
+    });
+    it('number', function () {
+      assert.equal("12", ServerConnector.objectToRequestString(12));
+    });
+    it('point', function () {
+      assert.equal("0.00,10.00", ServerConnector.objectToRequestString(new Point(0, 10)));
+    });
+    it('array of ids', function () {
+      assert.equal("1,4", ServerConnector.objectToRequestString([1, 4]));
+    });
+    it('not sorted array of ids', function () {
+      assert.equal("1,4,5", ServerConnector.objectToRequestString([5, 1, 4]));
+    });
+  });
+
+
 });

frontend-js/src/test/js/map/OverlayParser-test.js

@@ -42,5 +42,50 @@ describe('OverlayParser', function () {
       });
     });
   });
+  describe('containsMixedNewLineCharacters', function () {
+    it('normal file', function () {
+      return ServerConnector.sendGetRequest("testFiles/overlay/good.txt").then(function (fileContent) {
+        var parser = new OverlayParser();
+        assert.notOk(parser.containsMixedNewLineCharacters(fileContent));
+      });
+    });
+    it('windows/linux mix', function () {
+      var content = "line1\n\rline2\n";
+      var parser = new OverlayParser();
+      assert.ok(parser.containsMixedNewLineCharacters(content));
+    });
+
+    it('windows empty lines', function () {
+      var content = "line1\n\rline2\n\r\n\rline4";
+      var parser = new OverlayParser();
+      assert.notOk(parser.containsMixedNewLineCharacters(content));
+    });
+
+    it('windows/mac mix', function () {
+      var content = "line1\n\rline2\r";
+      var parser = new OverlayParser();
+      assert.ok(parser.containsMixedNewLineCharacters(content));
+    });
+
+    it('mac empty lines', function () {
+      var content = "line1\rline2\r\rline4";
+      var parser = new OverlayParser();
+      assert.notOk(parser.containsMixedNewLineCharacters(content));
+    });
+
+    it('windows/mac mix 2', function () {
+      var content = "line1\n\r\rline2\n\rline3";
+      var parser = new OverlayParser();
+      assert.ok(parser.containsMixedNewLineCharacters(content));
+    });
+
+    it('linux empty lines', function () {
+      var content = "line1\nline2\n\nline4";
+      var parser = new OverlayParser();
+      assert.notOk(parser.containsMixedNewLineCharacters(content));
+    });
+
+
+  });
 
 });

frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/POST_participantId=329167&token=MOCK_TOKEN_ID&

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\ No newline at end of file

model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java

@@ -221,7 +221,14 @@ public class ColorModelCommand extends ModelCommand {
         }
       }
       for (MiriamData md : schema.getMiriamData()) {
-        if (!element.getMiriamData().contains(md)) {
+        boolean found = false;
+        for (MiriamData elementMiriamData : element.getMiriamData()) {
+          if (elementMiriamData.getDataType().equals(md.getDataType())
+              && elementMiriamData.getResource().equals(md.getResource())) {
+            found = true;
+          }
+        }
+        if (!found) {
           return false;
         }
       }

model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java

@@ -360,6 +360,61 @@ public class ColorModelCommandTest extends CommandTestFunctions {
 
   }
 
+  @Test
+  public void testSpeciesMatchWithMiriamData() throws Exception {
+    try {
+      GenericColorSchema colorSchema = new GenericColorSchema();
+      colorSchema.setName("s1");
+      colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+      GenericColorSchema colorSchema2 = new GenericColorSchema();
+      colorSchema2.setName("s1");
+      colorSchema2.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7"));
+
+      GenericProtein species = new GenericProtein("id");
+      species.setName("s1");
+      species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+      List<ColorSchema> schemas = new ArrayList<>();
+      schemas.add(colorSchema);
+
+      ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+      assertTrue(factory.match(species, colorSchema));
+      assertFalse(factory.match(species, colorSchema2));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+