diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java
index 385b8c2ae7ed1765ba3621f774bee40231fbe403..2a39d1aaa82d7c747f37b9da7965e0623e19a6bd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java
@@ -159,8 +159,9 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
* {@link #referenceGenome}
* @param name
* {@link #name}
+ * @throws ReferenceGenomeConnectorException
*/
- private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) {
+ private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) throws ReferenceGenomeConnectorException {
this.url = url;
this.referenceGenome = referenceGenome;
this.name = name;
@@ -173,36 +174,36 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
}
};
}
+
}
@Override
public Void call() throws Exception {
getDbUtils().createSessionForCurrentThread();
try {
- ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
- for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
- if (mapping.getName().equals(name)) {
- throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
- }
- }
- if (!url.toLowerCase().endsWith("bb")) {
- throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
- }
+ ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
+ for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
+ if (mapping.getName().equals(name)) {
+ throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
+ }
+ }
+ if (!url.toLowerCase().endsWith("bb")) {
+ throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
+ }
ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
- mapping.setReferenceGenome(referenceGenome);
mapping.setName(name);
mapping.setSourceUrl(url);
referenceGenome.addReferenceGenomeGeneMapping(mapping);
- getReferenceGenomeGeneMappingDao().add(mapping);
- getReferenceGenomeGeneMappingDao().flush();
+ getReferenceGenomeDao().update(referenceGenome);
getReferenceGenomeDao().commit();
+ getReferenceGenomeDao().flush();
getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
@Override
public void setProgress(double progress) {
if (updater != null) {
updater.setProgress(progress);
}
- // we have to get the object because it's in separate thred
+ // we have to get the object because it's in separate thread
ReferenceGenomeGeneMapping temp = getReferenceGenomeGeneMappingDao().getById(mapping.getId());
temp.setDownloadProgress(progress);
getReferenceGenomeGeneMappingDao().update(temp);
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index e6ae7e3baaefc2db36fba1de9f8afbc399e94c82..61174790bda4d2a654ac21c8b3646e69a351d7ae 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -643,7 +643,8 @@ h1 {
.minerva-plugin-tab .minerva-menu-row button,
.minerva-edit-project-dialog .minerva-menu-row button,
.minerva-users-tab .minerva-menu-row button,
-.minerva-genome-tab .minerva-menu-row button {
+.minerva-genome-tab .minerva-menu-row button,
+.minerva-edit-genome-dialog .minerva-menu-row button {
margin: 5px;
}
@@ -1104,6 +1105,7 @@ input[type=file] {
background: #f5f5f5;
cursor: pointer;
}
+
#minervaAppDiv table.dataTable.hover tbody tr:hover,
#minervaAppDiv table.dataTable.display tbody tr:hover,
#minervaAppDiv table.dataTable.display tbody tr:hover > .sorting_1,
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 3163015862ba479d7b783a5e691ce8cb83aaf438..ed52d611712915b61ae5c970919e4f573fe19449 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -38,6 +38,7 @@ var SbmlParameter = require('./map/data/SbmlParameter');
var SecurityError = require('./SecurityError');
var SessionData = require('./SessionData');
var User = require('./map/data/User');
+var ValidationError = require('./ValidationError');
var PrivilegeType = require('./map/data/PrivilegeType');
var GuiConnector = require('./GuiConnector');
@@ -2433,7 +2434,14 @@ ServerConnector.addGeneMapping = function (params) {
name: params.mappingName,
url: params.mappingUrl
};
- return self.sendPostRequest(self.getReferenceGenomeGeneMappingsUrl(params), data);
+ return self.sendPostRequest(self.getReferenceGenomeGeneMappingsUrl(params), data).catch(function (e) {
+ if (e instanceof NetworkError && e.statusCode === HttpStatus.BAD_REQUEST) {
+ var content = JSON.parse(e.content);
+ throw new ValidationError(content.reason);
+ } else {
+ return self.processNetworkError(e);
+ }
+ });
};
/**
*
diff --git a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
index 60cb158713b861c8ebd85eb479d55e753fc3c4a5..cff98ee83e7a361e23f7d0b1215c0c043097afc0 100644
--- a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
@@ -32,6 +32,7 @@ function EditGenomeDialog(params) {
self.setReferenceGenome(params.referenceGenome);
$(self.getElement()).css({overflow: "hidden"});
+ $(self.getElement()).addClass("minerva-edit-genome-dialog");
self.createGui();
self.registerListenerType("onSave");
@@ -240,6 +241,18 @@ EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
menuRow.appendChild(addGeneMappingButton);
+ var refreshButton = Functions.createElement({
+ type: "button",
+ name: "saveGenome",
+ content: ' REFRESH',
+ onclick: function () {
+ return self.refresh();
+ },
+ xss: false
+ });
+
+ menuRow.appendChild(refreshButton);
+
return result;
};
@@ -259,7 +272,7 @@ EditGenomeDialog.prototype.onSaveClicked = function () {
genome.setVersion(self.getSelectedVersion());
return self.getServerConnector().addReferenceGenome(genome).then(function () {
return self.callListeners("onSave");
- }).catch(function(e){
+ }).catch(function (e) {
if (e instanceof ObjectExistsError) {
GuiConnector.alert("Reference genome already exists");
} else {
@@ -433,7 +446,7 @@ EditGenomeDialog.prototype.geneMappingToTableRow = function (geneMapping) {
var row = [];
row[0] = geneMapping.getName();
row[1] = geneMapping.getSourceUrl();
- row[2] = geneMapping.getProgress();
+ row[2] = geneMapping.getProgressStatus();
row[3] = "<button name='removeMapping' data='" + geneMapping.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
return row;
};
@@ -468,34 +481,40 @@ EditGenomeDialog.prototype.init = function () {
*/
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]);
- data.push(['Source url', Functions.createElement({type: "input", name: "genomeSourceUrl"}).outerHTML]);
- data.push(['Local url', Functions.createElement({type: "input", name: "genomeLocalUrl"}).outerHTML]);
- data.push(['Progress', Functions.createElement({type: "input", name: "genomeProgress"}).outerHTML]);
-
- 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);
+ var refreshReferenceGenomePromise = Promise.resolve();
+ if (!self.isNew()) {
+ refreshReferenceGenomePromise = self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()}).then(function (genome) {
+ self.setReferenceGenome(genome);
+ });
}
- //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 refreshReferenceGenomePromise.then(function () {
+ 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]);
+ data.push(['Source url', Functions.createElement({type: "input", name: "genomeSourceUrl"}).outerHTML]);
+ data.push(['Local url', Functions.createElement({type: "input", name: "genomeLocalUrl"}).outerHTML]);
+ data.push(['Progress', Functions.createElement({type: "input", name: "genomeProgress"}).outerHTML]);
+
+ 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);
+ return self._fillOrganismSelect(genome);
+ });
};
/**
@@ -522,6 +541,7 @@ EditGenomeDialog.prototype.destroy = function () {
/**
*
+ * @return {Promise}
*/
EditGenomeDialog.prototype.open = function () {
var self = this;
@@ -541,6 +561,8 @@ EditGenomeDialog.prototype.open = function () {
});
}
$(div).dialog("open");
+
+ return self.refresh();
};
/**
@@ -621,7 +643,7 @@ EditGenomeDialog.prototype.openAddGeneMapping = function () {
return self.refresh();
}).then(function () {
$(dialog).dialog('destroy').remove();
- });
+ }).catch(GuiConnector.alert);
},
'Cancel': function () {
$(this).dialog('destroy').remove();
diff --git a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
index afece10d70d1c7d0ee1dcb3574f75b270ccf6c8b..a6ed06d2aee54057ab17d2d929c6c7056ea90c5d 100644
--- a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
@@ -297,11 +297,9 @@ GenomeAdminPanel.prototype.showEditDialog = function (id) {
}
return self.getDialog(referenceGenome);
}).then(function (dialog) {
- dialog.open();
+ return dialog.open();
+ }).finally(function () {
GuiConnector.hideProcessing();
- }).catch(function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
});
};
@@ -314,11 +312,9 @@ GenomeAdminPanel.prototype.onAddClicked = function () {
GuiConnector.showProcessing();
var referenceGenome = new ReferenceGenome();
return self.getDialog(referenceGenome).then(function (dialog) {
- dialog.open();
- GuiConnector.hideProcessing();
- }).catch(function (error) {
+ return dialog.open();
+ }).finally(function () {
GuiConnector.hideProcessing();
- return Promise.reject(error);
});
};
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
index 1d5ec11c43558133f767b1aae3c2ec4e5a33f7db..3f765a66793971ea03d71699112df696057c7f2e 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
@@ -84,6 +84,27 @@ ReferenceGenomeGeneMapping.prototype.getSourceUrl = function () {
return this._sourceUrl;
};
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getProgressStatus = function () {
+ var progress = this.getProgress();
+ if (progress === 100) {
+ if (this.getLocalUrl() !== undefined) {
+ return "READY";
+ } else {
+ return "ERROR";
+ }
+ } else {
+ if (progress === undefined) {
+ return "N/A";
+ } else {
+ return progress.toFixed(2) + ' %';
+ }
+ }
+};
+
/**
*
* @param {string} url
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 84af369f43914b2b33e1256b69d63d30fb2cda8c..bcc6152d61139ae1b1d5d9f3734ad6016864a259 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
@@ -244,7 +244,7 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
try {
referenceGenomeService.addReferenceGenome(genomeType, organism, version, url);
return okStatus();
- } catch(ReferenceGenomeExistsException e) {
+ } catch (ReferenceGenomeExistsException e) {
throw new ObjectExistsException(e);
} catch (URISyntaxException e) {
throw new QueryException("Problem wih given uri", e);
@@ -262,6 +262,10 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
String name = getFirstValue(formData.get("name"));
String url = getFirstValue(formData.get("url"));
+ if (!url.toLowerCase().endsWith("bb")) {
+ throw new QueryException("Only big bed format files are supported but found: \"" + url + "\".");
+ }
+
referenceGenomeService.addReferenceGenomeGeneMapping(genome, name, url);
return okStatus();
} catch (URISyntaxException e) {