From 4042b4da0fde3a1f0ac28c77c7771d11f9e8ed22 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 3 Jul 2018 15:34:23 +0200
Subject: [PATCH] adding of reference genomes implemented
---
.../genome/ReferenceGenomeConnector.java | 4 +-
.../genome/UcscReferenceGenomeConnector.java | 1 +
frontend-js/src/main/js/ServerConnector.js | 61 +++++++-
.../src/main/js/gui/admin/EditGenomeDialog.js | 137 ++++++++++++++----
.../js/gui/admin/EditGenomeDialog-test.js | 105 +++++++++-----
...pe=UCSC&version=hg38&token=ADMIN_TOKEN_ID& | 1 +
.../token=ADMIN_TOKEN_ID& | 1 +
.../token=MOCK_TOKEN_ID& | 1 +
.../genomics/ReferenceGenomeController.java | 28 +++-
.../api/genomics/ReferenceGenomeRestImpl.java | 52 ++++++-
.../ReferenceGenomeControllerTest.java | 12 ++
11 files changed, 337 insertions(+), 66 deletions(-)
create mode 100644 frontend-js/testFiles/apiCalls/genomics/POST_organismId=9606&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg18%2FbigZips%2Fhg18.2bit&type=UCSC&version=hg38&token=ADMIN_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=ADMIN_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=MOCK_TOKEN_ID&
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
index fbfb32622f..33d279d315 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
@@ -127,7 +127,7 @@ public interface ReferenceGenomeConnector {
* @param version
* version of the reference genome
* @throws IOException
- * thrown when there is a problem with removeing file
+ * thrown when there is a problem with removing file
*/
void removeGenomeVersion(MiriamData organism, String version) throws IOException;
@@ -135,7 +135,7 @@ public interface ReferenceGenomeConnector {
* Returns url to the file that describes reference genome.
*
* @param organism
- * organism of redference genome
+ * organism of reference genome
* @param version
* version of the reference genome
* @return url to the file that describes reference genome
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
index 9af8f7fdc3..d95d98b5c9 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
@@ -387,6 +387,7 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
String remotePath = getGenomePath(organism, version);
FTPFile[] files = ftp.listFiles(remotePath);
for (FTPFile ftpFile : files) {
+ logger.debug(ftpFile.getName());
if (ftpFile.getName().endsWith(".2bit")) {
if (filename != null) {
logger.warn("More than one 2bit file found in a folder: " + remotePath + ". Using first: " + filename);
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index be25fb33fd..e11954790e 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -448,6 +448,24 @@ ServerConnector.getReferenceGenomeUrl = function (queryParams, filterParams) {
}
};
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} queryParams.version
+ * @param {Annotation} queryParams.organism
+ * @param {string} queryParams.type
+ * @param {Object} filterParams
+ *
+ * @returns {string}
+ */
+ServerConnector.getAvailableGenomeUrlsUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/taxonomies/" + queryParams.organism.getResource() + "/genomeTypes/" + queryParams.type + "/versions/" + queryParams.version
+ + ":getAvailableRemoteUrls",
+ params: filterParams
+ });
+};
+
/**
*
* @param {Object} queryParams
@@ -792,8 +810,8 @@ ServerConnector.getUsersUrl = function (queryParams, filterParams) {
/**
*
- * @param {Object} queryParams
- * @param {Object} filterParams
+ * @param {Object} [queryParams]
+ * @param {Object} [filterParams]
*
* @returns {string}
*/
@@ -2077,6 +2095,45 @@ ServerConnector.getReferenceGenome = function (params) {
}
};
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.version
+ * @param {Annotation} params.organism
+ * @param {string} params.type
+ *
+ * @returns {Promise<string[]>}
+ */
+ServerConnector.getAvailableGenomeUrls = function (params) {
+ var self = this;
+ var filterParams = {};
+ return self.sendGetRequest(self.getAvailableGenomeUrlsUrl(params, filterParams)).then(function (content) {
+ var result = [];
+ var raw = JSON.parse(content);
+ for (var i = 0; i < raw.length; i++) {
+ result.push(raw[i].url);
+ }
+ return result;
+ });
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @returns {Promise<ReferenceGenome>}
+ */
+ServerConnector.addReferenceGenome = function (genome) {
+ var self = this;
+ var data = {
+ organismId: genome.getOrganism().getResource(),
+ type: genome.getType(),
+ version: genome.getVersion(),
+ sourceUrl: genome.getSourceUrl()
+ };
+ return self.sendPostRequest(self.getReferenceGenomesUrl(), 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 3f0cf1646f..1987cc9ece 100644
--- a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
@@ -3,6 +3,7 @@
var Promise = require("bluebird");
var AbstractGuiElement = require('../AbstractGuiElement');
+var Annotation = require('../../map/data/Annotation');
var GuiConnector = require('../../GuiConnector');
var Functions = require('../../Functions');
@@ -175,6 +176,19 @@ EditGenomeDialog.prototype.createGeneralTabContent = function () {
});
result.appendChild(table);
+ $(table).on("change", "[name='genomeOrganismSelect']", function () {
+ return self._fillTypeSelect(self.getReferenceGenome(), self.getSelectedOrganism());
+ });
+
+ $(table).on("change", "[name='genomeTypeSelect']", function () {
+ return self._fillVersionSelect(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType());
+ });
+
+ $(table).on("change", "[name='genomeVersionSelect']", function () {
+ return self._fillUrl(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType(), self.getSelectedVersion());
+ });
+
+
var menuRow = Functions.createElement({
type: "div",
className: "minerva-menu-row",
@@ -217,7 +231,12 @@ EditGenomeDialog.prototype.onSaveClicked = function () {
if (!self.isNew()) {
return self.callListeners("onSave");
} else {
- return self.getServerConnector().updateReferenceGenome(self.getReferenceGenome()).then(function () {
+ var genome = self.getReferenceGenome();
+ genome.setSourceUrl(self.getSourceUrl());
+ genome.setOrganism(self.getSelectedOrganism());
+ genome.setType(self.getSelectedType());
+ genome.setVersion(self.getSelectedVersion());
+ return self.getServerConnector().addReferenceGenome(genome).then(function () {
return self.callListeners("onSave");
});
}
@@ -232,6 +251,7 @@ EditGenomeDialog.prototype._fillOrganismSelect = function (genome) {
var self = this;
return self.getServerConnector().getReferenceGenomeOrganisms().then(function (organisms) {
var genomeOrganismSelect = $("[name=genomeOrganismSelect]", self.getElement());
+ genomeOrganismSelect.empty();
var selectedOrganism;
if (self.isNew()) {
selectedOrganism = organisms[0];
@@ -255,7 +275,7 @@ EditGenomeDialog.prototype._fillOrganismSelect = function (genome) {
}));
});
genomeOrganismSelect.val(selectedOrganism.getResource());
- return selectedOrganism;
+ return self._fillTypeSelect(genome, selectedOrganism);
});
};
@@ -271,6 +291,8 @@ EditGenomeDialog.prototype._fillTypeSelect = function (genome, selectedOrganism)
return self.getServerConnector().getReferenceGenomeTypes({organism: selectedOrganism}).then(function (types) {
var genomeTypeSelect = $("[name=genomeTypeSelect]", self.getElement());
+ genomeTypeSelect.empty();
+
var selectedType;
if (self.isNew()) {
selectedType = types[0].type;
@@ -289,7 +311,7 @@ EditGenomeDialog.prototype._fillTypeSelect = function (genome, selectedOrganism)
}));
});
genomeTypeSelect.val(selectedType);
- return selectedType;
+ return self._fillVersionSelect(genome, selectedOrganism, selectedType);
})
};
@@ -307,8 +329,9 @@ EditGenomeDialog.prototype._fillVersionSelect = function (genome, selectedOrgani
organism: selectedOrganism,
type: selectedType
}).then(function (versions) {
-
var genomeVersionSelect = $("[name=genomeVersionSelect]", self.getElement());
+ genomeVersionSelect.empty();
+
var selectedVersion;
if (self.isNew()) {
selectedVersion = versions[0].version;
@@ -327,9 +350,52 @@ EditGenomeDialog.prototype._fillVersionSelect = function (genome, selectedOrgani
}));
});
genomeVersionSelect.val(selectedVersion);
+ return self._fillUrl(genome, selectedOrganism, selectedType, selectedVersion);
})
};
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {Annotation} organism
+ * @param {string} type
+ * @param {string} version
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillUrl = function (genome, organism, type, version) {
+ var self = this;
+ var genomeSourceUrlInput = $("[name=genomeSourceUrl]", self.getElement());
+ var genomeLocalUrlInput = $("[name=genomeLocalUrl]", self.getElement());
+ var genomeProgressInput = $("[name=genomeProgress]", self.getElement());
+ genomeLocalUrlInput.prop("disabled", true);
+ genomeProgressInput.val(genome.getDownloadProgressStatus());
+ genomeProgressInput.prop("disabled", true);
+ if (!self.isNew()) {
+ genomeSourceUrlInput.val(genome.getSourceUrl());
+ genomeSourceUrlInput.prop("disabled", true);
+
+ genomeLocalUrlInput.val(genome.getLocalUrl());
+ } else {
+ genomeSourceUrlInput.prop("disabled", false);
+
+ genomeLocalUrlInput.val("");
+ return self.getServerConnector().getAvailableGenomeUrls({
+ organism: organism,
+ type: type,
+ version: version
+ }).then(function (urls) {
+ if (urls.length > 0) {
+ genomeSourceUrlInput.val(urls[0]);
+ } else {
+ genomeSourceUrlInput.val("");
+ }
+ })
+ }
+ return Promise.resolve();
+}
+;
+
/**
*
@@ -364,27 +430,7 @@ EditGenomeDialog.prototype.init = function () {
dataTable.clear().rows.add(data).draw();
- var selectedOrganism, selectedType;
- return self._fillOrganismSelect(genome).then(function (organism) {
- selectedOrganism = organism;
- return self._fillTypeSelect(genome, selectedOrganism);
- }).then(function (type) {
- selectedType = type;
- return self._fillVersionSelect(genome, selectedOrganism, selectedType);
- }).then(function (version) {
- var genomeSourceUrlInput = $("[name=genomeSourceUrl]", self.getElement());
- genomeSourceUrlInput.val(genome.getSourceUrl());
- genomeSourceUrlInput.prop("disabled", true);
-
- var genomeLocalUrlInput = $("[name=genomeLocalUrl]", self.getElement());
- genomeLocalUrlInput.val(genome.getLocalUrl());
- genomeLocalUrlInput.prop("disabled", true);
-
- var genomeProgressInput = $("[name=genomeProgress]", self.getElement());
- genomeProgressInput.val(genome.getDownloadProgressStatus());
- genomeProgressInput.prop("disabled", true);
-
- });
+ return self._fillOrganismSelect(genome);
};
EditGenomeDialog.prototype.destroy = function () {
@@ -427,4 +473,45 @@ EditGenomeDialog.prototype.close = function () {
$(self.getElement()).dialog("close");
};
+/**
+ *
+ * @returns {Annotation}
+ */
+EditGenomeDialog.prototype.getSelectedOrganism = function () {
+ var self = this;
+ return new Annotation({
+ resource: ($("[name='genomeOrganismSelect']", self.getElement()).val()).toString(),
+ link: '',
+ id: 0,
+ type: ''
+ })
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSelectedType = function () {
+ var self = this;
+ return ($("[name='genomeTypeSelect']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSelectedVersion = function () {
+ var self = this;
+ return ($("[name='genomeVersionSelect']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSourceUrl = function () {
+ var self = this;
+ return ($("[name='genomeSourceUrl']", self.getElement()).val()).toString();
+};
+
module.exports = EditGenomeDialog;
diff --git a/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js b/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js
index 5eb04f7f35..c0f889d02d 100644
--- a/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js
@@ -13,45 +13,70 @@ var chai = require('chai');
var assert = chai.assert;
var expect = chai.expect;
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @returns {EditGenomeDialog}
+ */
+function createDialog(genome) {
+ return new EditGenomeDialog({
+ element: testDiv,
+ referenceGenome: genome,
+ customMap: null,
+ serverConnector: ServerConnector
+ });
+}
+
describe('EditGenomeDialog', function () {
describe('init', function () {
it('new genome', function () {
- var dialog;
- var project;
var genome = new ReferenceGenome();
- return ServerConnector.getProject().then(function (result) {
- project = result;
- dialog = new EditGenomeDialog({
- element: testDiv,
- project: project,
- referenceGenome: genome,
- customMap: null,
- serverConnector: ServerConnector
- });
- return dialog.init();
- }).then(function () {
- dialog.destroy();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ return dialog.destroy();
});
});
});
+ it('on organism change', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ var element = $("[name='genomeOrganismSelect']")[0];
+ return helper.triggerJqueryEvent(element, "change");
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+
+ it('on type change', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ var element = $("[name='genomeTypeSelect']")[0];
+ return helper.triggerJqueryEvent(element, "change");
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+
+ it('on version change', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ var element = $("[name='genomeVersionSelect']")[0];
+ return helper.triggerJqueryEvent(element, "change");
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+
describe('click cancel', function () {
it('new genome', function () {
- var dialog;
- var project;
var genome = new ReferenceGenome();
- return ServerConnector.getProject().then(function (result) {
- project = result;
- dialog = new EditGenomeDialog({
- element: testDiv,
- project: project,
- referenceGenome: genome,
- customMap: null,
- serverConnector: ServerConnector
- });
- return dialog.init();
- }).then(function () {
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
return dialog.open();
}).then(function () {
return $("[name=cancelGenome]", testDiv)[0].onclick();
@@ -64,13 +89,12 @@ describe('EditGenomeDialog', function () {
describe('click save', function () {
it('existing genome', function () {
var dialog;
- return ServerConnector.getReferenceGenome({organism:"9606", type:"UCSC",version:"hg38"}).then(function (genome) {
- dialog = new EditGenomeDialog({
- element: testDiv,
- referenceGenome: genome,
- customMap: null,
- serverConnector: ServerConnector
- });
+ return ServerConnector.getReferenceGenome({
+ organism: "9606",
+ type: "UCSC",
+ version: "hg38"
+ }).then(function (genome) {
+ dialog = createDialog(genome);
return dialog.init();
}).then(function () {
return dialog.open();
@@ -80,6 +104,19 @@ describe('EditGenomeDialog', function () {
dialog.destroy();
});
});
+
+ it('new genome', function () {
+ helper.loginAsAdmin();
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ return dialog.open();
+ }).then(function () {
+ return $("[name=saveGenome]", testDiv)[0].onclick();
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
});
});
diff --git a/frontend-js/testFiles/apiCalls/genomics/POST_organismId=9606&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg18%2FbigZips%2Fhg18.2bit&type=UCSC&version=hg38&token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/POST_organismId=9606&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg18%2FbigZips%2Fhg18.2bit&type=UCSC&version=hg38&token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000..9e26dfeeb6
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/POST_organismId=9606&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg18%2FbigZips%2Fhg18.2bit&type=UCSC&version=hg38&token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000..c97ec2eab9
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"url":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..c97ec2eab9
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"url":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit"}]
\ No newline at end of file
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 b8c950515a..63b8088bd8 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
@@ -6,13 +6,16 @@ import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
+import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.CookieValue;
import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import javassist.tools.rmi.ObjectNotFoundException;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Configuration;
@@ -35,6 +38,17 @@ public class ReferenceGenomeController extends BaseController {
return referenceGenomeController.getReferenceGenome(token, organism, type, version);
}
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}:getAvailableRemoteUrls", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getRemoteUrls(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type, //
+ @PathVariable(value = "version") String version//
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getRemoteUrls(token, organism, type, version);
+ }
+
@RequestMapping(value = "/genomics/taxonomies/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public List<Map<String, Object>> getGenomeTaxonomies(//
@@ -43,6 +57,15 @@ public class ReferenceGenomeController extends BaseController {
return referenceGenomeController.getReferenceGenomeTaxonomies(token);
}
+ @RequestMapping(value = "/genomics/", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addGenome(//
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ return referenceGenomeController.addReferenceGenome(formData, token);
+ }
+
@RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public List<Map<String, Object>> getGenomeTaxonomyTypes(//
@@ -68,8 +91,9 @@ public class ReferenceGenomeController extends BaseController {
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenomes(token);
}
-
- @RequestMapping(value = "/genomics/{genomeId}/", method = { RequestMethod.DELETE }, produces = { MediaType.APPLICATION_JSON_VALUE })
+
+ @RequestMapping(value = "/genomics/{genomeId}/", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> removeGenome(//
@PathVariable(value = "genomeId") String genomeId, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token //
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 cedb3cc467..cd515a62d5 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
@@ -2,6 +2,7 @@ package lcsb.mapviewer.api.genomics;
import java.io.FileNotFoundException;
import java.io.IOException;
+import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -13,6 +14,7 @@ import java.util.TreeMap;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
+import org.springframework.util.MultiValueMap;
import lcsb.mapviewer.annotation.cache.BigFileCache;
import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
@@ -25,7 +27,6 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
@@ -69,6 +70,30 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
}
}
+ public List<Map<String, Object>> getRemoteUrls(String token, String organismId, String type, String version)
+ throws SecurityException, QueryException, ObjectNotFoundException {
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ try {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ String url = referenceGenomeService.getUrlForGenomeVersion(genomeType, organism, version);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ if (url != null) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("url", url);
+ result.add(row);
+ }
+ return result;
+ } catch (IllegalArgumentException e) {
+ throw new QueryException("Cannot find type: " + type);
+ }
+ }
+
private Map<String, Object> genomeToMap(ReferenceGenome genome) {
Map<String, Object> result = new TreeMap<>();
result.put("organism", super.createAnnotation(genome.getOrganism()));
@@ -190,4 +215,29 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
return okStatus();
}
+ public Map<String, Object> addReferenceGenome(MultiValueMap<String, Object> formData, String token)
+ throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+
+ String organismId = getFirstValue(formData.get("organismId"));
+ String type = getFirstValue(formData.get("type"));
+ String version = getFirstValue(formData.get("version"));
+ String url = getFirstValue(formData.get("sourceUrl"));
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ try {
+ referenceGenomeService.addReferenceGenome(genomeType, organism, version, url);
+ return okStatus();
+ } catch (URISyntaxException e) {
+ throw new QueryException("Problem wih given uri", e);
+ }
+ }
+
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
index d1bb8e0b1f..35e85fa7db 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
@@ -98,6 +98,18 @@ public class ReferenceGenomeControllerTest extends RestTestFunctions {
}
}
+ @Test
+ public void testGetRemoteUrls() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getRemoteUrls(adminToken, "9606", "UCSC", "hg18");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testGetAllDowloadedReferenceGenomes() throws Exception {
try {
--
GitLab