From 27931cdb64f61a964164a8ac2e48a6ee49122185 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 3 Jul 2018 17:27:43 +0200
Subject: [PATCH] adding of gene mappings implemented
---
frontend-js/src/main/js/ServerConnector.js | 32 ++++++++++
.../src/main/js/gui/admin/EditGenomeDialog.js | 59 ++++++++++++++++++-
.../genomics/ReferenceGenomeController.java | 10 ++++
.../api/genomics/ReferenceGenomeRestImpl.java | 18 ++++++
4 files changed, 118 insertions(+), 1 deletion(-)
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index e8e1ce157c..bd787b7f03 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -464,6 +464,21 @@ ServerConnector.getReferenceGenomeGeneMappingUrl = function (queryParams, filter
});
};
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} queryParams.genomeId
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomeGeneMappingsUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/" + queryParams.genomeId + "/geneMapping/",
+ params: filterParams
+ });
+};
+
/**
*
* @param {Object} queryParams
@@ -2109,6 +2124,23 @@ ServerConnector.getReferenceGenome = function (params) {
}
};
+
+/**
+ *
+ * @param {Object} params
+ * @param {string|number} params.genomeId
+ * @param {string} params.mappingName
+ * @param {string} params.mappingUrl
+ * @returns {PromiseLike}
+ */
+ServerConnector.addGeneMapping = function (params) {
+ var self = this;
+ var data = {
+ name: params.mappingName,
+ url: params.mappingUrl
+ };
+ return self.sendPostRequest(self.getReferenceGenomeGeneMappingsUrl(params), data);
+};
/**
*
* @param {Object} params
diff --git a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
index f178839c4f..24aded0d9d 100644
--- a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
@@ -297,6 +297,25 @@ EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
}).catch(GuiConnector.alert);
});
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var addGeneMappingButton = Functions.createElement({
+ type: "button",
+ name: "saveGenome",
+ content: '<span class="ui-icon ui-icon-disk"></span> ADD GENE MAPPING',
+ onclick: function () {
+ return self.openAddGeneMapping();
+ },
+ xss: false
+ });
+
+ menuRow.appendChild(addGeneMappingButton);
+
return result;
};
@@ -497,7 +516,7 @@ EditGenomeDialog.prototype.init = function () {
var detailsTable = $("[name=detailsTable]", self.getElement())[0];
- var dataTable = $(detailsTable).DataTable({
+ $(detailsTable).DataTable({
columns: [{
title: "Name"
}, {
@@ -630,4 +649,42 @@ EditGenomeDialog.prototype.getSourceUrl = function () {
return ($("[name='genomeSourceUrl']", self.getElement()).val()).toString();
};
+/**
+ *
+ */
+EditGenomeDialog.prototype.openAddGeneMapping = function () {
+ var self = this;
+ var html = '<form style="z-index:10000"><span>Name: </span><input type="text" name="gene-mapping-name"><br>' +
+ '<span>Url: </span><input type="text" name="gene-mapping-url"><br></form>';
+ $(html).dialog({
+ modal: true,
+ title: "Add gene mapping",
+ close: function () {
+ $(this).dialog('destroy').remove();
+ },
+ buttons: {
+ 'ADD': function () {
+ var dialog = this;
+ var name = $('input[name="gene-mapping-name"]').val().toString();
+ var url = $('input[name="gene-mapping-url"]').val().toString();
+ return self.getServerConnector().addGeneMapping({
+ genomeId: self.getReferenceGenome().getId(),
+ mappingName: name,
+ mappingUrl: url
+ }).then(function () {
+ return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
+ }).then(function (referenceGenome) {
+ self.setReferenceGenome(referenceGenome);
+ return self.refresh();
+ }).then(function () {
+ $(dialog).dialog('destroy').remove();
+ });
+ },
+ 'Cancel': function () {
+ $(this).dialog('destroy').remove();
+ }
+ }
+ });
+};
+
module.exports = EditGenomeDialog;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
index 0be38d8fa4..cbcb47bcad 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
@@ -111,4 +111,14 @@ public class ReferenceGenomeController extends BaseController {
return referenceGenomeController.removeGeneMapping(genomeId,mappingId, token);
}
+ @RequestMapping(value = "/genomics/{genomeId}/geneMapping/", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addGeneMapping(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ return referenceGenomeController.addGeneMapping(formData, genomeId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
index bc71b2447c..b47cf24709 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
@@ -241,6 +241,24 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
}
}
+ public Map<String, Object> addGeneMapping(MultiValueMap<String, Object> formData, String genomeId, String token)
+ throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+
+ int id = Integer.parseInt(genomeId);
+ try {
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
+ String name = getFirstValue(formData.get("name"));
+ String url = getFirstValue(formData.get("url"));
+ referenceGenomeService.addReferenceGenomeGeneMapping(genome, name, url);
+ return okStatus();
+ } catch (URISyntaxException e) {
+ throw new QueryException("Problem wih given uri", e);
+ }
+ }
+
public Map<String, Object> removeGeneMapping(String genomeId, String mappingId, String token)
throws SecurityException, IOException, ObjectNotFoundException {
if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
--
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