Commit 17a8bf77 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge remote-tracking branch 'origin/devel_13.2.x' into merge-13.2.0

parents e9f40baa 3e5f3475
Pipeline #13392 failed with stage
in 9 minutes and 50 seconds
......@@ -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)
......
......@@ -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"
},
......
......@@ -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");
......
......@@ -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);
}
}
});
......
......@@ -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;
......
......@@ -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({
......
......@@ -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);
......
......@@ -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();
......
......@@ -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));
}
}
#TYPE=gen
value identifier Chebi
-0,943978048 HGNC:11138
-0,941309505 CHEBI:15377
1 CHEBI:15376
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