diff --git a/CHANGELOG b/CHANGELOG
index a8ef67f3248b745a13ab77d99645193f99ad2aa0..4e1287a8609cdd05bd11df92736483a4a56f4d34 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,14 +1,14 @@
minerva (14.0.0~alpha.1) unstable; urgency=low
* Feature removal: support for tomcat7 removed (#828)
* Small improvement: debian package can be installed on debian:buster (#879)
- * Bug fix: REST API bioEntities:search method didn't limit results to the
+ * Bug fix: REST API bioEntities:search method didn't limit results to the
submodel id (#860)
* Bug fix: Empty Overlay colours were not preserved during export to
CellDesigner (#714)
- * Bug fix: some project couldn't be accessed due to problem with migration of
+ * Bug fix: some project couldn't be accessed due to problem with migration of
reaction with unknown boolean operator (#880)
* Bug fix: problem with unloading plugin is properly handled (#884)
- * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
+ * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
loaded plugins (#885)
* Bug fix: link to molart was brokwn (#886)
* Bug fix: context menu visualization fixed
@@ -17,16 +17,16 @@ minerva (14.0.0~alpha.1) unstable; urgency=low
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 13 Aug 2019 21:00:00 +0200
minerva (14.0.0~alpha.0) unstable; urgency=low
- * Feature: security layer redesigned - privilege types and scope changed
+ * Feature: security layer redesigned - privilege types and scope changed
(#636, #624)
* Feature: log4j is replaced with log4j2 logging mechanism (#291)
* Feature: database installed via debian package is done via dbconfig-commons
(#469)
* Feature: Replaced connection pool manager C3P0 with better maintained
- Hikari - restart of postgresql database doesn't require restart of tomcat
+ Hikari - restart of postgresql database doesn't require restart of tomcat
(#564)
* Feature removal: BioCompendium annotator removed (#32)
- * Small improvement: anonymous login is no longer required - each API query
+ * Small improvement: anonymous login is no longer required - each API query
outside session is authorized with anonymous user privileges (#629)
* Small improvement: bcrypt is used for password encryption (#387)
* Small improvement: caching is active by default for new users when
@@ -34,14 +34,14 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
* Small improvement: when removing overlay in admin panel there is a
confirmation dialog (#696)
* Small improvement: overlay name is obligatory (#698)
- * Small improvement: list of projects in admin panel contains creation date
+ * Small improvement: list of projects in admin panel contains creation date
(#447)
* Small improvement: links in list of publications open in new tab (#447)
* Small improvement: target gene in search panel contains also information
about type of database that identifies the target (#66)
- * Small improvement: redundant 'references' field in gene variants data
+ * Small improvement: redundant 'references' field in gene variants data
overlay is now deprecated (#850)
- * Small improvement: information about deprecated columns in data overlay is
+ * Small improvement: information about deprecated columns in data overlay is
visible in overlay list (#838)
* Small improvement: publication list is resizeable (#740)
* Small improvement: user list on project edit dialog is sortable (#808)
@@ -60,6 +60,21 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 09 Aug 2019 10:00:00 +0200
+minerva (13.1.4) stable; urgency=medium
+ * Bug fix:search by drugs didn't check synonyms in chembl database
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 21 Aug 2019 17:00:00 +0200
+
+minerva (13.1.3) stable; urgency=medium
+ * Bug fix: refreshing list of projects or list of users doesn't change active
+ page (#870)
+ * Bug fix: submap list must be selected to export from every submap (#874)
+ * Bug fix: export map as image properly uses bottom limit (#875)
+ * Bug fix: reaction info window wasn't closed on CLEAR (#876)
+ * Bug fix: name of the uploaded file is displayed when adding overlay (#849)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 14 Aug 2019 17:00:00 +0200
+
minerva (13.1.2) stable; urgency=medium
* Bug fix: Information about problematic zip file is more specific (#865)
* Bug fix: Url didn't contain list of opened plugins and they weren't reload
@@ -77,7 +92,7 @@ minerva (13.1.1) stable; urgency=medium
* Bug fix: user wasn't logged out in all tabs when the log out event appeard
in only one of them (#847)
- -- Piotr Gawron <piotr.gawron@uni.lu> Tue, 2 Jul 2019 19:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu> Tue, 2 Jul 2019 19:00:00 +0200
minerva (13.1.0) stable; urgency=medium
* Feature: annotators are more flexible - you can define set of input and
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 37a429c6f0d4c4be1e3d3a0500ec74179f091fea..0f553690da62c7dd3bb5fdcc9298c51120d20ebb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -52,6 +52,12 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
* Url that access data of drug identified by name.
*/
private static final String DRUG_NAME_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?pref_name__exact=";
+
+ /**
+ * Url that access data of drug identified by name.
+ */
+ private static final String DRUG_SYNONYM_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?molecule_synonyms__molecule_synonym__iexact=";
+
/**
* Url that access target by identifier.
*/
@@ -324,29 +330,22 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
String page = getWebPageContent(accessUrl);
Document document = XmlParser.getXmlDocumentFromString(page);
- Node response = XmlParser.getNode("response", document.getChildNodes());
- Node molecules = XmlParser.getNode("molecules", response.getChildNodes());
-
- NodeList list = molecules.getChildNodes();
-
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("molecule")) {
- if (drug == null) {
- drug = parseDrug(node);
- } else {
- logger.warn("More drugs than one found for query: " + query);
- }
- }
- }
+ List<Drug> drugs = extractDrugsFromDocument(document);
+ if (drugs.size()==0) {
+ accessUrl = DRUG_SYNONYM_API_URL + name;
+ page = getWebPageContent(accessUrl);
+ document = XmlParser.getXmlDocumentFromString(page);
+ drugs = extractDrugsFromDocument(document);
+ }
+ if (drugs.size()>1) {
+ logger.warn("More drugs than one found for query: " + query);
}
- if (drug == null) {
+ if (drugs.size() == 0) {
return null;
}
- setCacheValue(query, getDrugSerializer().objectToString(drug));
- return drug;
+ setCacheValue(query, getDrugSerializer().objectToString(drugs.get(0)));
+ return drugs.get(0);
} catch (IOException e) {
throw new DrugSearchException("Problem with accessing CHEMBL database", e);
} catch (InvalidXmlSchemaException e) {
@@ -354,6 +353,24 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
}
+ private List<Drug> extractDrugsFromDocument(Document document) throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
+ Node response = XmlParser.getNode("response", document.getChildNodes());
+ Node molecules = XmlParser.getNode("molecules", response.getChildNodes());
+
+ NodeList list = molecules.getChildNodes();
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("molecule")) {
+ result.add(parseDrug(node));
+ }
+ }
+ }
+ return result;
+ }
+
@Override
public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms)
throws DrugSearchException {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index dfe8729b8fc362065fc9077d4eec3fe113d3f79a..ff25cddd78eac023de8094f8f4a40b6bf8b80dab 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -877,4 +877,16 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testFindDrugBryBrandName() throws Exception {
+ try {
+ Drug drug = chemblParser.findDrug("picato");
+ assertNotNull(drug);
+ assertEquals("CHEMBL1863513", drug.getSources().get(0).getResource());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index c9f0c38d09a9ba606522a135ec7586ded1a2a82a..96d4490165607dfddfa0709bca89c8b7d049f362 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -95,9 +95,7 @@ AddOverlayDialog.prototype.createGui = function () {
name: "overlay-file"
});
fileInput.addEventListener("change", function () {
- return self.processFile(fileInput.files[0]).then(function () {
- $(fileInput).val("");
- }).catch(GuiConnector.alert);
+ return self.processFile(fileInput.files[0]).catch(GuiConnector.alert);
}, false);
content.appendChild(fileInput);
content.appendChild(guiUtils.createNewLine());
@@ -294,9 +292,10 @@ AddOverlayDialog.prototype.open = function () {
return self.addOverlay().then(function (result) {
$(dialog).dialog("close");
return result;
- }, function (error) {
+ }).catch(function (error) {
GuiConnector.hideProcessing();
if (error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST) {
+ $("[name='overlay-file']", self.getElement()).val("");
var errorMessage = JSON.parse(error.content);
GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
} else if (error instanceof SecurityError) {
diff --git a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
index dcac66b096da9038fe252ab6b68368cd2becb53f..c5124c44b01f6c12ce63f0d355e46d56a78f915c 100644
--- a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
@@ -346,7 +346,9 @@ MapsAdminPanel.prototype.addUpdateListener = function (project) {
var data = row.data();
if (data[0].indexOf(">" + project.getProjectId() + "<") >= 0) {
self.projectToTableRow(project, data, user);
+ var page = dataTable.page();
row.data(data).draw();
+ dataTable.page(page);
}
}
});
diff --git a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
index 6de9dbcf6e3d527e1099a29bb47de20ba79b5688..735848903e887a4c2cd7383650aa6a2638a857fc 100644
--- a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
@@ -303,11 +303,13 @@ UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
var listener = function () {
var login = Functions.escapeSelector(user.getLogin());
self.userToTableRow(user, dataTableRow);
- var row = $($("[name='usersTable']", self.getElement())[0]).DataTable().row("#" + login);
+ var dataTable =$("[name='usersTable']", self.getElement()).DataTable();
+ var row = dataTable.row("#" + login);
if (row.length > 0) {
+ var page = dataTable.page();
row.data(dataTableRow).draw();
+ dataTable.page(page);
}
-
};
listener.listenerName = listenerName;
user.addListener("onreload", listener);
diff --git a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
index e22bb9beb066340a497a1d30d156571db2c352de..636e2d2d954f197f158c8814c07711c8784f76af 100644
--- a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
@@ -223,7 +223,7 @@ AbstractExportPanel.prototype._createSelectSubmapDiv = function (models) {
var id = model.getId();
var row = Functions.createElement({
type: "li",
- content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + name + "\" value=\"" + id + "\" />" + name + "</label></div>",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + name + "\" value=\"" + id + "\" checked/>" + name + "</label></div>",
xss: false
});
choicesContainer.appendChild(row);
diff --git a/frontend-js/src/main/js/gui/export/ElementExportPanel.js b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
index a1ef96c581466c2b2fe626ee99dfd64c485d1662..54b04e95c464dc31c90243b00a1a537968ca2e64 100644
--- a/frontend-js/src/main/js/gui/export/ElementExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
@@ -95,7 +95,7 @@ ElementExportPanel.prototype.createResponseString = function () {
var promises = [];
for (var i = 0; i < models.length; i++) {
var model = models[i];
- if (submapIds.length === 0 || $.inArray(model.getId(), submapIds) >= 0) {
+ if ($.inArray(model.getId(), submapIds) >= 0) {
promises.push(model.getAliases({
type: types,
complete: true,
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
index 46a728fac879d268378b4817743a8258ac147cf0..bb07cfd58fba8c6fdb9933441ee2cb0c8c20708a 100644
--- a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -147,10 +147,8 @@ function matchReaction(reaction, elementIds, reactionTypes, submapIds) {
if ($.inArray(reaction.getType(), reactionTypes) === -1) {
return false;
}
- if (submapIds.length > 0) {
- if ($.inArray(reaction.getModelId(), submapIds) === -1) {
- return false;
- }
+ if ($.inArray(reaction.getModelId(), submapIds) === -1) {
+ return false;
}
var count = 0;
reaction.getElements().forEach(function (element) {
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index 1ceef72193d908c7fb5ee6679b08bd3e3f77d3e6..192a87aa79bcb1fd80363f8a003b1a98fa3cd45e 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -207,7 +207,7 @@ AbstractCustomMap.prototype.registerMapClickEvents = function () {
var y1 = Math.max(0, topLeft.y);
var x2 = Math.min(self.getModel().getWidth(), rightBottom.x);
- var y2 = Math.max(self.getModel().getHeight(), rightBottom.y);
+ var y2 = Math.min(self.getModel().getHeight(), rightBottom.y);
var polygon = "";
polygon += x1 + "," + y1 + ";";
diff --git a/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js b/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js
index 6ee77ee55986f8721bb867c97b5d81b45482e6e7..e4eab7e4c4df3de0c3b83c6ae9d654c6b77ddfa2 100644
--- a/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js
+++ b/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js
@@ -12,6 +12,8 @@ function OpenLayerPolyline(options) {
var self = this;
+ self.registerListenerType("onHide");
+
if (options.strokeColor === undefined) {
options.strokeColor = "#000000";
}
@@ -74,7 +76,8 @@ OpenLayerPolyline.prototype.show = function () {
};
OpenLayerPolyline.prototype.hide = function () {
- return this.getOpenLayersPolyline().setStyle(new ol.style.Style({}));
+ this.getOpenLayersPolyline().setStyle(new ol.style.Style({}));
+ return this.callListeners("onHide");
};
OpenLayerPolyline.prototype.isShown = function () {
diff --git a/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js b/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js
index c9634456b480961b6dae875c690b872ac8b45370..8ab253ea9171735c35c34b7eaf4bbf5734ca5ce5 100644
--- a/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js
+++ b/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js
@@ -228,7 +228,12 @@ MarkerSurfaceCollection.prototype.createSurfaceForDbOverlay = function (element,
onClick: onclickFunctions
});
result.addListener("onClick", function () {
- return map.getTopMap().openInfoWindowForIdentifiedElement(element);
+ return map.getTopMap().openInfoWindowForIdentifiedElement(element).then(function (infoWindow) {
+ result.getMapCanvasObjects()[0].addListener("onHide", function () {
+ return infoWindow._infoWindow.hide();
+ });
+ return infoWindow;
+ });
});
self.putSurface({element: element, overlay: dbOverlay}, result);
if (self.getMap().isInitialized()) {
diff --git a/persist/src/main/resources/db/migration/13.1.4/V13.1.4.20190821__remove_chembl_cache.sql b/persist/src/main/resources/db/migration/13.1.4/V13.1.4.20190821__remove_chembl_cache.sql
new file mode 100644
index 0000000000000000000000000000000000000000..6aea6b38443948a2f8999010f401d3a6f41cb16a
--- /dev/null
+++ b/persist/src/main/resources/db/migration/13.1.4/V13.1.4.20190821__remove_chembl_cache.sql
@@ -0,0 +1 @@
+delete from cache_query_table where type in (select id from cache_type_table where class_name ='lcsb.mapviewer.annotation.services.ChEMBLParser');
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
index 9ea2461a03ab8f64551a0f482ae9a8d522bd82f1..85312d412a9923a8bd8d73a79ab6c47a65b46170 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
@@ -174,9 +174,15 @@ public class DrugService extends DbSearchService implements IDrugService {
if (name.trim().equals("")) {
return null;
}
+ DrugAnnotation secondParser = chEMBLParser;
Drug drug = null;
try {
drug = drugBankParser.findDrug(name);
+
+ if (drug==null) {
+ drug = chEMBLParser.findDrug(name);
+ secondParser = drugBankParser;
+ }
if (drug != null) {
removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
}
@@ -190,13 +196,13 @@ public class DrugService extends DbSearchService implements IDrugService {
// * search for name
searchNames.add(name);
if (drug != null && drug.getName() != null) {
- // * search for name of a drug in drugbanke
+ // * search for name of a drug in drugbank
searchNames.add(drug.getName());
// * search for all synonyms found in drugbank
// searchNames.addAll(drug.getSynonyms());
}
for (String string : searchNames) {
- Drug drug2 = chEMBLParser.findDrug(string);
+ Drug drug2 = secondParser.findDrug(string);
if (drug2 != null) {
removeUnknownOrganisms(drug2, searchCriteria.getOrganisms());
// don't add drugs that were already found
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
index ed04915bfc95cbdb94b8628b3a70b6a0bb6addd7..d7635648ecf2c98ca89313d31b4b90905840ec34 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
@@ -42,6 +42,17 @@ public class DrugServiceTest extends ServiceTestFunctions {
assertNull(drug);
}
+ @Test
+ public void testGetIstodax() throws Exception {
+ try {
+ Drug drug = drugService.getByName("istodax", new DbSearchCriteria());
+ assertEquals(2, drug.getSources().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testGetTargets() throws Exception {
long count = searchHistoryDao.getCount();