diff --git a/CHANGELOG b/CHANGELOG
index 251ddb898c68b8b7a17fe6951e914c70ae29239d..95f20518edee3f653205853ae3310967b746df6d 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -2,40 +2,40 @@ minerva (14.0.0~beta.0) unstable; urgency=low
* Small improvement: sorting by columns that doesn't make sense in admin
panel is disabled (#895)
* Small improvement: version of minerva is visible in map browser panel
- * Small improvement: small info about annotator details is available in
+ * Small improvement: small info about annotator details is available in
select anntoators dialog (#923)
- * Small improvement: CellDesigner layers are always visualized as pathways
+ * Small improvement: CellDesigner layers are always visualized as pathways
(#813)
* Small improvement: setting "Modify project| checkbox automatically select
"View project" checkbox when editing privileges (#920)
* Small improvement: notification email uses minerva name and id of affected
project (#926)
- * Small improvement: information about person who uploaded project is visible
+ * Small improvement: information about person who uploaded project is visible
in list of projects (#927)
* Small improvement: user role introduced in edit user dialog (#924)
* Small improvement: tab with list of glyps is available when adding project
with glyphs (#925)
- * Small improvement: BackgroundColor parameter should be assigned using ":"
+ * Small improvement: BackgroundColor parameter should be assigned using ":"
character (#929)
* Bug fix: work on FF Private Window mode could cause logout or raise an
error on when opening new tab with minerva (#892)
- * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
+ * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
Error" (#889)
* Bug fix: user without admin right can accept terms of service (#893)
* Bug fix: edit project dialog verifies organism id (#914)
- * Bug fix: user without admin or curator privileges shouldn't be able to
+ * Bug fix: user without admin or curator privileges shouldn't be able to
check logs (#894)
* Bug fix: user without admin or curator privileges had issues with accesing
and removing data overlays (#897, #898, #899, #903)
- * Bug fix: privilege checking on updating privileges, data overlays were not
+ * Bug fix: privilege checking on updating privileges, data overlays were not
sufficient and could lead to access escalation
* Bug fix: user without privileges had edit map input options enabled
- * Bug fix: user without privileges had edit map input options for managing
+ * Bug fix: user without privileges had edit map input options for managing
project users
* Bug fix: curator couldn't update data overlay in some situations (#905)
- * Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome",
+ * Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome",
"Edit Project", "Edit User" (#881)
- * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
+ * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
properly (#907)
* Bug fix: proper line type for boolean reaction is used on the whole
reaction (#908)
@@ -48,7 +48,7 @@ minerva (14.0.0~beta.0) unstable; urgency=low
case the type was not specified in the input file (#906)
* Bug fix: list of types when copying from annotators contains only types
that are selectable in the dialog (#911)
- * Bug fix: remove of data overlay didn't update numbering of data overlays
+ * Bug fix: remove of data overlay didn't update numbering of data overlays
that are still in the system (#918)
* Bug fix: too long name for data overlay in info window is trimmed (#919)
* Bug fix: too long name in general overlay list is wrapped (#857)
@@ -122,10 +122,17 @@ 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
+minerva (13.2.0) stable; urgency=medium
+ * Small improvement: MolArt v1.4 is used which provide information from
+ PredictProtein (#913)
+ * Bug fix: search by drugs didn't check synonyms in chembl database
+ * Bug fix: verification of overlay type added (#917)
+ * Bug fix: opening edit project/user dialog returned list of users/projects
+ to the 1st page (#909)
+ * Bug fix: show element title option wasn't influencing title visibility
+ (#910)
- -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 21 Aug 2019 17:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 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
@@ -135,7 +142,7 @@ minerva (13.1.3) stable; urgency=medium
* 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
+ -- 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)
diff --git a/frontend-js/package.json b/frontend-js/package.json
index d8b8209834eb9862075f149960c91f2cb5a2c1f7..7370e19452841feab07a6febca535e4c3af6f2f4 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -31,7 +31,7 @@
"mkdirp": "^0.5.1",
"mocha": "^3.5.3",
"mock-local-storage": "^1.1.8",
- "molart": "1.3.2",
+ "molart": "1.4.0",
"stream-to-blob": "^1.0.1",
"uglifyjs": "^2.4.10"
},
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index 1c3859e2f86204a2d043669c52dc9bc3e0aba44b..e9d20fe7b0e2115e44e38828f21b71cdff976efe 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -164,6 +164,9 @@ AddOverlayDialog.prototype.processFile = function (file) {
}
if (overlay.getType() !== undefined) {
+ if ($("option[value='" + overlay.getType() + "']", typeSelect).length === 0) {
+ GuiConnector.warn("Invalid type: " + overlay.getType());
+ }
self.setType(overlay.getType());
} else {
self.setType("GENERIC");
diff --git a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
index fa98fe394c68171defb5f24301867c9c58d1e546..70b7104bc35ca9fdcb58ebbd64ce734a2a50a9ee 100644
--- a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
@@ -376,7 +376,7 @@ MapsAdminPanel.prototype.addUpdateListener = function (project) {
self.projectToTableRow(project, data, user);
var page = dataTable.page();
row.data(data).draw();
- dataTable.page(page);
+ dataTable.page(page).draw(false);
}
}
});
diff --git a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
index 2ac1ec90f623c731351aafaf62f56cb11b57c6fc..16ed1e9c5da0cbd66af3f723bfa660a20f6bb1b9 100644
--- a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
@@ -311,7 +311,7 @@ UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
if (row.length > 0) {
var page = dataTable.page();
row.data(dataTableRow).draw();
- dataTable.page(page);
+ dataTable.page(page).draw(false);
}
};
listener.listenerName = listenerName;
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 658d425042b1e8467a8e3ef18ac7de636b633643..da747c20ddcf36094da0e52265f922a38760672d 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -823,9 +823,17 @@ GuiUtils.prototype.createAliasElement = function (params) {
}));
}
- div.appendChild(this.createParamLine({label: alias.getType() + ": ", value: alias.getName()}));
+ div.appendChild(this.createParamLine({
+ label: alias.getType() + ": ",
+ className: self._configurationOptionToClassName(ConfigurationType.SHOW_ELEMENT_TITLE),
+ value: alias.getName()
+ }));
if (alias.getModelId() !== self.getMap().getId()) {
- div.appendChild(self.createSubMapLink({label: "In submap: ", mapId: alias.getModelId()}));
+ div.appendChild(self.createSubMapLink({
+ label: "In submap: ",
+ className: self._configurationOptionToClassName(ConfigurationType.SHOW_ELEMENT_TITLE),
+ mapId: alias.getModelId()
+ }));
}
}
div.appendChild(self.createSubMapLink({
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index af525309e8582bc2d4dc5f58c798b457c04f3be2..3cd4e6053c6b811ec5108ee1164221bed2381157 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -85,7 +85,14 @@ public class ColorSchemaReader {
return readGenericColorSchema(colorInputStream);
}
} else {
- ColorSchemaType type = ColorSchemaType.valueOf(params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
+ ColorSchemaType type = null;
+ try {
+ type = ColorSchemaType.valueOf(params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
+ } catch (IllegalArgumentException e) {
+ String options = StringUtils.join(ColorSchemaType.values(), ", ");
+ throw new InvalidColorSchemaException("Invalid overlay type: "
+ + params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) + ". Allowed options: " + options);
+ }
if (type == null) {
logger.warn("Unknown type of layout file: " + params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
return readGenericColorSchema(colorInputStream);
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 39aabb78ae490005522c4f4393d945cb03c09386..40056af478d1acb22596d0753817896859b5bf30 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
@@ -53,6 +53,17 @@ public class DrugServiceTest extends ServiceTestFunctions {
}
}
+ @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();
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index e97c9420f00cd4570dca48c15b4cc2777135d124..798fa15e868747d459cc52314aa6a107fc4d00c4 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -367,4 +367,13 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
overlay.setInputData(file);
assertEquals(0, reader.getDeprecatedColumns(overlay).size());
}
+
+ @Test(expected = InvalidColorSchemaException.class)
+ public void testReadColorSchemaWithInvalidType() throws Exception {
+ FileInputStream fis = new FileInputStream("testFiles/coloring/invalidType.txt");
+ FileInputStream fis2 = new FileInputStream("testFiles/coloring/invalidType.txt");
+ ColorSchemaReader reader = new ColorSchemaReader();
+ reader.readColorSchema(fis, TextFileUtils.getHeaderParametersFromFile(fis2));
+
+ }
}
diff --git a/service/testFiles/coloring/invalidType.txt b/service/testFiles/coloring/invalidType.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c669cb9dadcb5bce4cc3110ce6672c8accdef3bb
--- /dev/null
+++ b/service/testFiles/coloring/invalidType.txt
@@ -0,0 +1,5 @@
+#TYPE=gen
+value identifier Chebi
+-0,943978048 HGNC:11138
+-0,941309505 CHEBI:15377
+1 CHEBI:15376