possibility to remove gene mapping

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

@@ -448,6 +448,22 @@ ServerConnector.getReferenceGenomeUrl = function (queryParams, filterParams) {
   }
 };
 
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} queryParams.genomeId
+ * @param {string} queryParams.mappingId
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomeGeneMappingUrl = function (queryParams, filterParams) {
+  return this.getApiUrl({
+    type: "genomics/" + queryParams.genomeId + "/geneMapping/" + queryParams.mappingId + "/",
+    params: filterParams
+  });
+};
+
 /**
  *
  * @param {Object} queryParams
@@ -1278,8 +1294,6 @@ ServerConnector.getReferenceGenomes = function () {
       result.push(genome)
     }
     return result;
-  }).catch(function (error) {
-    return self.processNetworkError(error);
   });
 };
 
@@ -2071,7 +2085,7 @@ ServerConnector.getPublications = function (params) {
  * @param {string} [params.version]
  * @param {string} [params.organism]
  * @param {string} [params.type]
- * @param {string} [params.genomeId]
+ * @param {string|number} [params.genomeId]
  *
  * @returns {Promise}
  */
@@ -2133,6 +2147,19 @@ ServerConnector.addReferenceGenome = function (genome) {
   return self.sendPostRequest(self.getReferenceGenomesUrl(), data);
 };
 
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.genomeId
+ * @param {string} params.mappingId
+ *
+ * @returns {Promise}
+ */
+ServerConnector.removeReferenceGenomeGeneMapping = function (params) {
+  var self = this;
+  return self.sendDeleteRequest(self.getReferenceGenomeGeneMappingUrl(params));
+};
+
 
 /**
  *

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

@@ -92,11 +92,13 @@ EditGenomeDialog.prototype.createGui = function () {
   tabDiv.appendChild(tabContentDiv);
 
   self.createGeneralTab(tabMenuDiv, tabContentDiv);
+  self.createGeneMappingTab(tabMenuDiv, tabContentDiv);
   $("a", tabMenuDiv).bind("click", function () {
     //workaround for some css issues...
     tabDiv.style.top = "40px";
     tabDiv.style.bottom = "10px";
   });
+
 };
 
 /**
@@ -115,6 +117,22 @@ EditGenomeDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDi
 
 };
 
+/**
+ *
+ * @param {HTMLElement} tabMenuDiv
+ * @param {HTMLElement} tabContentDiv
+ */
+EditGenomeDialog.prototype.createGeneMappingTab = function (tabMenuDiv, tabContentDiv) {
+  var self = this;
+  self.addTab({
+    tabMenuDiv: tabMenuDiv,
+    tabContentDiv: tabContentDiv,
+    name: "GENE MAPPING",
+    content: self.createGeneMappingTabContent()
+  });
+
+};
+
 var id_counter = 0;
 
 /**
@@ -222,6 +240,66 @@ EditGenomeDialog.prototype.createGeneralTabContent = function () {
   return result;
 };
 
+/**
+ *
+ * @returns {HTMLElement}
+ */
+EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
+
+  var self = this;
+
+  var result = Functions.createElement({
+    type: "div",
+    style: "margin-top:10px;"
+  });
+
+  var geneMappingTable = Functions.createElement({
+    type: "table",
+    name: "geneMappingTable",
+    className: "display",
+    style: "width:100%"
+  });
+  result.appendChild(geneMappingTable);
+
+  // noinspection JSUnusedGlobalSymbols
+  $(geneMappingTable).DataTable({
+    columns: [{
+      title: 'Name'
+    }, {
+      title: 'Source'
+    }, {
+      title: 'Progress'
+    }, {
+      title: 'Remove',
+      orderable: false
+    }],
+    order: [[1, "asc"]]
+  });
+
+  $(geneMappingTable).on("click", "[name='removeMapping']", function () {
+    var button = this;
+    return self.askConfirmRemoval({
+      title: "INFO",
+      content: "Do you really want to remove this gene mapping?",
+      input: false
+    }).then(function (param) {
+      if (param.status) {
+        return self.getServerConnector().removeReferenceGenomeGeneMapping({
+          mappingId: $(button).attr("data"),
+          genomeId: self.getReferenceGenome().getId()
+        }).then(function () {
+          return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
+        }).then(function (referenceGenome) {
+          self.setReferenceGenome(referenceGenome);
+          return self.refresh();
+        });
+      }
+    }).catch(GuiConnector.alert);
+  });
+
+  return result;
+};
+
 /**
  *
  * @returns {Promise|PromiseLike}
@@ -397,6 +475,19 @@ EditGenomeDialog.prototype._fillUrl = function (genome, organism, type, version)
 ;
 
 
+/**
+ *
+ * @param {ReferenceGenomeGeneMapping} geneMapping
+ * @returns {Array}
+ */
+EditGenomeDialog.prototype.geneMappingToTableRow = function (geneMapping) {
+  var row = [];
+  row[0] = geneMapping.getName();
+  row[1] = geneMapping.getSourceUrl();
+  row[2] = geneMapping.getProgress();
+  row[3] = "<button name='removeMapping' data='" + geneMapping.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
+  return row;
+};
 /**
  *
  * @returns {Promise}
@@ -417,10 +508,18 @@ EditGenomeDialog.prototype.init = function () {
     searching: false,
     bInfo: false
   });
-  var data = [];
+
+  return self.refresh();
+};
+
+EditGenomeDialog.prototype.refresh = function () {
+  var self = this;
 
   var genome = self.getReferenceGenome();
 
+  var dataTable = $("[name=detailsTable]", self.getElement()).DataTable();
+  var data = [];
+
   data.push(['Organism', Functions.createElement({type: "select", name: "genomeOrganismSelect"}).outerHTML]);
   data.push(['Type', Functions.createElement({type: "select", name: "genomeTypeSelect"}).outerHTML]);
   data.push(['Version', Functions.createElement({type: "select", name: "genomeVersionSelect"}).outerHTML]);
@@ -430,9 +529,22 @@ EditGenomeDialog.prototype.init = function () {
 
   dataTable.clear().rows.add(data).draw();
 
+  dataTable = $("[name=geneMappingTable]", self.getElement()).DataTable();
+  data = [];
+  var page = dataTable.page();
+
+  for (var i = 0; i < genome.getGeneMappings().length; i++) {
+    var geneMapping = genome.getGeneMappings()[i];
+    var rowData = self.geneMappingToTableRow(geneMapping);
+    data.push(rowData);
+  }
+  //it should be simplified, but I couldn't make it work
+  dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+
   return self._fillOrganismSelect(genome);
 };
 
+
 EditGenomeDialog.prototype.destroy = function () {
   var self = this;
   var div = self.getElement();
@@ -442,6 +554,10 @@ EditGenomeDialog.prototype.destroy = function () {
     $(detailsTable).DataTable().destroy();
   }
 
+  var geneMappingTable = $("[name=geneMappingTable]", div)[0];
+  if ($.fn.DataTable.isDataTable(geneMappingTable)) {
+    $(geneMappingTable).DataTable().destroy();
+  }
 
   if ($(div).hasClass("ui-dialog-content")) {
     $(div).dialog("destroy");

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

@@ -23,6 +23,8 @@ function ReferenceGenome(javaObject) {
         this._geneMapping.push(new ReferenceGenomeGeneMapping(javaObject.geneMapping[i]));
       }
     }
+  } else {
+    this._geneMapping = [];
   }
 }
 

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

@@ -7,19 +7,106 @@ function ReferenceGenomeGeneMapping(javaObject) {
   } else {
     this.setUrl(javaObject.sourceUrl);
   }
+  this.setLocalUrl(javaObject.localUrl);
+  this.setSourceUrl(javaObject.sourceUrl);
+  this.setProgress(javaObject.downloadProgress);
+  this.setId(javaObject.idObject);
 }
 
-ReferenceGenomeGeneMapping.prototype.setName = function(name) {
+/**
+ *
+ * @param {string} name
+ */
+ReferenceGenomeGeneMapping.prototype.setName = function (name) {
   this._name = name;
 };
-ReferenceGenomeGeneMapping.prototype.setUrl = function(url) {
-  this._url = url;
-};
-ReferenceGenomeGeneMapping.prototype.getName = function() {
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getName = function () {
   return this._name;
 };
-ReferenceGenomeGeneMapping.prototype.getUrl = function() {
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setUrl = function (url) {
+  this._url = url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getUrl = function () {
   return this._url;
 };
 
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setLocalUrl = function (url) {
+  this._localUrl = url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getLocalUrl = function () {
+  return this._localUrl;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getSourceUrl = function () {
+  return this._sourceUrl;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setSourceUrl = function (url) {
+  this._sourceUrl = url;
+};
+
+/**
+ *
+ * @param {number} progress
+ */
+ReferenceGenomeGeneMapping.prototype.setProgress = function (progress) {
+  this._progress = progress;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenomeGeneMapping.prototype.getProgress = function () {
+  return this._progress;
+};
+
+/**
+ *
+ * @param {number} id
+ */
+ReferenceGenomeGeneMapping.prototype.setId = function (id) {
+  this._id = id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenomeGeneMapping.prototype.getId = function () {
+  return this._id;
+};
+
 module.exports = ReferenceGenomeGeneMapping;

frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js

@@ -8,6 +8,7 @@ var ValidationError = require('../../../../main/js/ValidationError');
 var ServerConnector = require('../../ServerConnector-mock');
 
 var logger = require('../../logger');
+var Promise = require('bluebird');
 
 var chai = require('chai');
 var assert = chai.assert;
@@ -37,8 +38,38 @@ describe('EditGenomeDialog', function () {
         return dialog.destroy();
       });
     });
+    it('existing', function () {
+      helper.loginAsAdmin();
+      var dialog;
+      return ServerConnector.getReferenceGenome({genomeId: 154}).then(function (genome) {
+        dialog = createDialog(genome);
+        return dialog.init();
+      }).then(function () {
+        return dialog.destroy();
+      });
+    });
   });
 
+  it('removeMapping', function () {
+    helper.loginAsAdmin();
+    var dialog;
+    return ServerConnector.getReferenceGenome({genomeId: 154}).then(function (genome) {
+      dialog = createDialog(genome);
+      return dialog.init();
+    }).then(function () {
+      dialog.askConfirmRemoval = function () {
+        return Promise.resolve({status: true});
+      };
+      assert.equal(0, logger.getWarnings().length);
+
+      var element = $("[name='removeMapping']")[0];
+      return helper.triggerJqueryEvent(element, "click");
+    }).then(function () {
+      return dialog.destroy();
+    });
+  });
+
+
   it('on organism change', function () {
     var genome = new ReferenceGenome();
     var dialog = createDialog(genome);

frontend-js/testFiles/apiCalls/genomics/154/DELETE_token=ADMIN_TOKEN_ID&

+{}
\ No newline at end of file

frontend-js/testFiles/apiCalls/genomics/154/geneMapping/97/DELETE_token=ADMIN_TOKEN_ID&

+{}
\ No newline at end of file

frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID&

-[{"downloadProgress":100.0,"geneMapping":[],"idObject":43,"localUrl":null,"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":517528,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=8822","resource":"8822","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/bigZips/aptMan1.2bit","type":"UCSC","version":"aptMan1"},{"downloadProgress":100.0,"geneMapping":[{"downloadProgress":100.0,"localUrl":null,"name":"refGene","sourceUrl":"http://pg-sandbox.uni.lu/data/refGene.txt.bb"}],"idObject":154,"localUrl":null,"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":523719,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit","type":"UCSC","version":"hg19"},{"downloadProgress":100.0,"geneMapping":[],"idObject":1563,"localUrl":"../minerva-big//5280/hg38.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":927074,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit","type":"UCSC","version":"hg38"}]
\ No newline at end of file
+[{"downloadProgress":100.0,"geneMapping":[{"downloadProgress":100.0,"idObject":97,"localUrl":null,"name":"refGene","sourceUrl":"http://pg-sandbox.uni.lu/data/refGene.txt.bb"}],"idObject":154,"localUrl":null,"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":523719,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit","type":"UCSC","version":"hg19"},{"downloadProgress":100.0,"geneMapping":[],"idObject":1563,"localUrl":"../minerva-big//5280/hg38.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":927074,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit","type":"UCSC","version":"hg38"},{"downloadProgress":100.0,"geneMapping":[],"idObject":1829,"localUrl":"../minerva-big//9387/hg18.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1150729,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit","type":"UCSC","version":"hg18"}]
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java

@@ -101,4 +101,14 @@ public class ReferenceGenomeController extends BaseController {
     return referenceGenomeController.removeGenome(genomeId, token);
   }
 
+  @RequestMapping(value = "/genomics/{genomeId}/geneMapping/{mappingId}/", method = { RequestMethod.DELETE }, produces = {
+      MediaType.APPLICATION_JSON_VALUE })
+  public Map<String, Object> removeGeneMapping(//
+      @PathVariable(value = "genomeId") String genomeId, //
+      @PathVariable(value = "mappingId") String mappingId, //
+      @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+  ) throws SecurityException, IOException, lcsb.mapviewer.api.ObjectNotFoundException {
+    return referenceGenomeController.removeGeneMapping(genomeId,mappingId, token);
+  }
+
 }
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java

@@ -133,6 +133,7 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
     result.put("localUrl", getLocalUrl(mapping.getSourceUrl()));
     result.put("sourceUrl", mapping.getSourceUrl());
     result.put("name", mapping.getName());
+    result.put("idObject", mapping.getId());
     return result;
   }
 
@@ -240,4 +241,27 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
     }
   }
 
+  public Map<String, Object> removeGeneMapping(String genomeId, String mappingId, String token)
+      throws SecurityException, IOException, ObjectNotFoundException {
+    if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+      throw new SecurityException("Access denied");
+    }
+    ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
+    if (genome == null) {
+      throw new ObjectNotFoundException("Genome doesn't exist");
+    }
+    int id = Integer.parseInt(mappingId);
+    ReferenceGenomeGeneMapping geneMapping = null;
+    for (ReferenceGenomeGeneMapping mapping : genome.getGeneMapping()) {
+      if (mapping.getId() == id) {
+        geneMapping = mapping;
+      }
+    }
+    if (geneMapping == null) {
+      throw new ObjectNotFoundException("Gene mapping doesn't exist");
+    }
+    referenceGenomeService.removeReferenceGenomeGeneMapping(geneMapping);
+    return okStatus();
+  }
+
 }