diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 31c2b6e4986d6415f2d8d69ba701507390fd1faf..22bd3a98c2fe66599d07565a911ecfc819f669d9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -392,3 +392,36 @@ test_deploy_with_db_without_superadmin_rights:
- test 200 = $(curl --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
- test 200 = $(curl --write-out %{http_code} --silent --output /dev/null --cookie cookie.txt http://localhost:8080/minerva/api/projects/)
+test_postgres_9_3_compatibility:
+ image: maven:3.6.0-jdk-8
+ services:
+ - postgres:9.3
+ stage: test
+ script:
+ - mkdir /etc/minerva/
+ - cp test-db-ci.properties /etc/minerva/db.properties
+ - mvn -DskipTests=true clean install -pl persist -am
+ - mvn test -pl persist
+
+test_postgres_10_compatibility:
+ image: maven:3.6.0-jdk-8
+ services:
+ - postgres:10
+ stage: test
+ script:
+ - mkdir /etc/minerva/
+ - cp test-db-ci.properties /etc/minerva/db.properties
+ - mvn -DskipTests=true clean install -pl persist -am
+ - mvn test -pl persist
+
+test_postgres_11_compatibility:
+ image: maven:3.6.0-jdk-8
+ services:
+ - postgres:11
+ stage: test
+ script:
+ - mkdir /etc/minerva/
+ - cp test-db-ci.properties /etc/minerva/db.properties
+ - mvn -DskipTests=true clean install -pl persist -am
+ - mvn test -pl persist
+
diff --git a/CHANGELOG b/CHANGELOG
index 091c93583ce78d5f461a679db9ed90cc3d0c5ba1..2eef00a6cea62514d0d7b9f221d56e9b25267ace 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,138 +1,45 @@
minerva (12.3.0~alpha.0) unstable; urgency=low
- * Feature: annotators are more flexible - you can define set of input and
+ * Feature: annotators are more flexible - you can define set of input and
outputs used by annotator (#617)
* Small improvement: validation of the organism and disease id on map upload
added (#618)
- * Small improvement: added current username next to logout button in admin
+ * Small improvement: added current username next to logout button in admin
panel (#660)
- * Small improvement: New comment dialog does not contain content of previous
+ * Small improvement: New comment dialog does not contain content of previous
comment dialog (#680)
* Small improvement: Left logo is configurable (#731)
* Small improvement: Plugin API provides list of overview images (#702)
* Small improvement: Plugin API allows to show/hide overview images (#702)
* Small improvement: Plugin API allows to trigger search on the map (#702)
* Small improvement: Plugin API allows to clear search results on map (#702)
- * Small improvement: edit/remove project button is disabled until project is
+ * Small improvement: edit/remove project button is disabled until project is
uploaded (#683)
- * Small improvement: warning about capslock is visible on login page when
+ * Small improvement: warning about capslock is visible on login page when
necessary (#658)
- * Small improvement: names of columns in data overlay are unified: no
+ * Small improvement: names of columns in data overlay are unified: no
whitespace, "_" used as separator (#596)
* Small improvement: list of references in drug panel contains PUBMED prefix
(#666)
- * Small improvement: passwords to email account and ldap are not sent over
+ * Small improvement: passwords to email account and ldap are not sent over
API (#732)
- * Small improvement: reactant/product/modifier specific colors are parsed
+ * Small improvement: reactant/product/modifier specific colors are parsed
properly from CellDesigner file (#597)
* Small improvement: Info tab contains information about disease and
organism when info is provided
* Small improvement: Info tab provides information about model annotations
and submap tabs provide information about submaps annotations if applicable
(#591)
- * Bug fix: progress bar of gene genome mapping upload is refreshing properly
+ * Bug fix: progress bar of gene genome mapping upload is refreshing properly
(#728)
- * Bug fix: when editing project Disease and Organism could not be removed
+ * Bug fix: when editing project Disease and Organism could not be removed
(#616)
- * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and
- "Unknown Inhibition" reactions (#664)
- * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
+ * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and
+ "Unknown Inhibition" reactions (#664)
+ * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
slightly separated from target phenotype (#664)
-minerva (12.2.0~beta.2) unstable; urgency=medium
- * Bug fix: order of the overlays is defined explicitly also for general
- overlays (#684)
- * Bug fix: files are saved in proper folder (#694, #670)
- * Bug fix: removing comments in a project asked for confirmation twice after
- edit project dialog for specific project was opened; closed and opened
- again (#697)
- * Bug fix: clicking on compartment border inside pathway should return
- compartment, not a pathway (#324)
- * Bug fix: clicking outside of the element sometimes resulted with the
- invalid element highlighted (#324)
- * Bug fix: parent compartment/pathway use proper type name in left panel
- (#324)
- * Bug fix: editing/removing project requires Map Management privilege (#681)
- * Bug fix: when removeAllListeners is called list of registered listeners is
- cleaned (#687)
- * Bug fix: when plugin is removed the html elements associated with it are
- removed as well (#686)
- * Bug fix: when creating new user default privileges are set properly (#692)
- * Bug fix: import from SBML issue - reaction with product and modifier being
- the same element caused exception (#703)
- * Bug fix: plugin can be added after plugin has been removed in admin plugin
- panel (#686)
- * Bug fix: too many annotations (>=100) caused misaligning in the left panel
- (#708)
- * Bug fix: text was outside the popup window (#711)
- * Bug fix: custom semantic zooming contains multiple overlays checkbox was
- disabled (#715)
- * Bug fix: export to svg contains viewBox info (#716)
- * Bug fix: import from sbml with layout could crash when two elements
- occupied the exact same position (#717)
- * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
- * Bug fix: Safari sometimes cached server responses and used wrong data, for
- example in admin panel configuration tab (#719)
- * Bug fix: description of transcription site is centered (#720)
- * Bug fix: selecting too few parameters in export doesn't throw reportable
- error (#721)
- * Bug fix: changes in selected checkbox in add project dialog block UI (#722)
- * Bug fix: providing invalid overlay id in url could break minerva (#726)
- * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
- * Bug fix: Editing project with images and submaps could cause a problem
- (#725)
- * Bug fix: opening map with invalid id shows proper error message (#724)
- * Bug fix: Fixing an issue where search panel was not properly resized on
- expansion (#682)
- * Small improvement: highlighting table rows in admin panel uses better
- contrast color (#706)
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 20 Feb 2019 14:00:00 +0200
-
-minerva (12.2.0~beta.1) unstable; urgency=medium
- * Small improvement: list of publication can be filtered by submap (#614)
- * Small improvement: report bug utility shows confirmation dialog on success
- (#648)
- * Small improvement: size of add overlay window adjusted to show more data
- without scrollbars (#657)
- * Small improvement: all popup dialogs in the app have dialog specific css
- class names (#665)
- * Bug fix: loading icon is not overlapping input in the search panel (#404)
- * Bug fix: position of transcription sites in genes are computed properly
- (#553)
- * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
- (#626)
- * Bug fix: layout exported to SBML can be properly visualized by COPASI
- (#654)
- * Bug fix: working with too many maps within the single session could crash
- connection to server (#651)
- * Bug fix: invalid pubmed id could crash listing/downloading publications
- (#656)
- * Bug fix: icons in safari sometimes disappear (#661)
- * Bug fix: downloading reference genome for the second time resulted in an
- error (#670)
- * Bug fix: plugin validation in admin panel improved to catch more problems
- (#672)
- * Bug fix: drawing corrupted heterodimer association in CellDesigner could
- crash map upload (#673)
- * Bug fix: custom semantic zooming didn't work with pathways imported from
- CellDesigner layers (#678)
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 7 Feb 2019 14:00:00 +0200
-
-minerva (12.2.0~beta.0) unstable; urgency=medium
+minerva (12.2.0) stable; urgency=medium
* Feature: bug report utility
- * Small improvement: JS plugin can create listener that is triggered on
- search results focus change
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 23 Jan 2019 15:00:00 +0200
-
-minerva (12.2.0~alpha.1) unstable; urgency=medium
- * Bug fix: problems with SBML-CellDesigner translation fixed
- * Bug fix: gitlab CI tests fixed
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 17 Jan 2019 15:00:00 +0200
-
-minerva (12.2.0~alpha.0) unstable; urgency=medium
* Feature: url GET parameters support all kind of search and selected overlays
highlight
* Feature: user can create custom logging configuration in file
@@ -144,6 +51,15 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
file formats
* Feature: current state of the browsed map is reflected in the url (position,
zoom, overlays, search queries, etc.)
+ * Small improvement: highlighting table rows in admin panel uses better
+ contrast color (#706)
+ * Small improvement: list of publication can be filtered by submap (#614)
+ * Small improvement: size of add overlay window adjusted to show more data
+ without scrollbars (#657)
+ * Small improvement: all popup dialogs in the application have dialog
+ specific css class names (#665)
+ * Small improvement: JS plugin can create listener that is triggered on
+ search results focus change
* Small improvement: export to SBML includes unit factors
* Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
* Small improvement: genetics information allows to provide information about
@@ -178,6 +94,47 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
* Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
email account is provided
* Small improvement: Plugin API allows to show/hide data overlays
+ * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
+ * Bug fix: migration scripts are compatibile with postgres 9.3 version that
+ is default on Ubuntu 14 (#762)
+ * Bug fix: update/remove button is disabled when user has no privileges for
+ managing overlays (#742)
+ * Bug fix: when user cannot manage users information in overlays and users
+ tab in edit project dialog is provided instead of hiding tabs (#756)
+ * Bug fix: removing comments in a project asked for confirmation twice after
+ edit project dialog for specific project was opened; closed and opened
+ again (#697)
+ * Bug fix: editing/removing project requires Map Management privilege (#681)
+ * Bug fix: when removeAllListeners is called list of registered listeners is
+ cleaned (#687)
+ * Bug fix: when plugin is removed the html elements associated with it are
+ removed as well (#686)
+ * Bug fix: when creating new user default privileges are set properly (#692)
+ * Bug fix: plugin can be added after plugin has been removed in admin plugin
+ panel (#686)
+ * Bug fix: too many annotations (>=100) caused misaligning in the left panel
+ (#708)
+ * Bug fix: export to svg contains viewBox info (#716)
+ * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
+ * Bug fix: Safari sometimes cached server responses and used wrong data, for
+ example in admin panel configuration tab (#719)
+ * Bug fix: description of transcription site is centered (#720)
+ * Bug fix: selecting too few parameters in export doesn't throw reportable
+ error (#721)
+ * Bug fix: providing invalid overlay id in url could break minerva (#726)
+ * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
+ * Bug fix: opening map with invalid id shows proper error message (#724)
+ * Bug fix: Fixing an issue where search panel was not properly resized on
+ expansion (#682)
+ * Bug fix: loading icon is not overlapping input in the search panel (#404)
+ * Bug fix: position of transcription sites in genes are computed properly
+ (#553)
+ * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
+ (#626)
+ * Bug fix: working with too many maps within the single session could crash
+ connection to server (#651)
+ * Bug fix: drawing corrupted heterodimer association in CellDesigner could
+ crash map upload (#673)
* Bug fix: export to CellDesigner align inhibition reaction properly
* Bug fix: export/import to/from SBML handles Heterodimer Association
reaction properly
@@ -193,9 +150,9 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
* Bug fix: type of the data overlay can be defined in the file content
(useful when uploading genetic variants)
* Bug fix: CLEAR button clears comment checkbox if necessary
- * Bug fix: minerva install problem on ubuntu 16 fixed
+ * Bug fix: minerva install problem on ubuntu 18 fixed
- -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 11 Jan 2019 12:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu> Mon, 25 Mar 2019 17:00:00 +0200
minerva (12.1.8) stable; urgency=medium
* Bug fix: add a project reset users custom overlays limit to default (#679)
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index 416421e54fbafe1ce757c904c24d632326a0d771..a99d1a4ac0775f5de79591abac9c2e8ab5a6e819 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -616,7 +616,7 @@ Plugin tabs
float: left;
}
-.minerva-top-checkbox-div input {
+.minerva-top-checkbox-div input[type=checkbox] {
margin-top: 12px;
display: inline;
float: left;
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 8390cbf4bd3d74d9d5d97f5f9201dcefe42a853d..049db1560a4e506ac9579738afca1d778efee4cf 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -788,10 +788,10 @@ AddProjectDialog.prototype.bindProjectUploadPreferences = function (user, type,
var value = user.getPreferences().getProjectUpload()[type];
element.prop('checked', value);
- GuiConnector.showProcessing();
element.change(function () {
var data = new UserPreferences();
data.getProjectUpload()[type] = element.is(":checked");
+ GuiConnector.showProcessing();
return ServerConnector.updateUserPreferences({
user: user,
preferences: data
diff --git a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
index 80548ba60b8aac9ca0387eee13b2f437a444029d..0b3073e53bc609711965a6d6c22ebbd7d3b8553e 100644
--- a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
@@ -641,7 +641,7 @@ EditProjectDialog.prototype.refreshOverlays = function () {
return self.setOverlays(overlays);
});
} else {
- guiUtils.hideTab(self, $(".minerva-project-overlays-tab", self.getElement())[0]);
+ guiUtils.disableTab($(".minerva-project-overlays-tab", self.getElement())[0], "You have no privileges to manage users data");
}
});
};
@@ -671,7 +671,7 @@ EditProjectDialog.prototype.refreshUsers = function () {
return self.setUsers(users);
});
} else {
- guiUtils.hideTab(self, $(".minerva-project-users-tab", self.getElement())[0]);
+ guiUtils.disableTab($(".minerva-project-users-tab", self.getElement())[0], "You have no privileges to manage users data");
}
});
};
@@ -774,9 +774,13 @@ EditProjectDialog.prototype.userToTableRow = function (user, columns) {
* @returns {Array}
*/
EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
+ var self = this;
var row = [];
var id = overlay.getId();
var creatorSelect;
+
+ var loggedUser = null;
+
if (overlay.getCreator() === "") {
creatorSelect = "<select name='creator-" + id + "' value=''>";
} else {
@@ -795,6 +799,10 @@ EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
creatorSelect += "<option value='" + user.getLogin() + "' " + selected + ">" + user.getLogin() + "("
+ user.getName() + " " + user.getSurname() + ")</option>";
+
+ if (user.getLogin() === self.getServerConnector().getSessionData().getLogin()) {
+ loggedUser = user;
+ }
}
creatorSelect += "</select>";
@@ -825,8 +833,15 @@ EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
row[4] = defaultOverlayCheckbox;
row[5] = creatorSelect;
row[6] = downloadSourceButton;
- row[7] = "<button name='saveOverlay' data='" + id + "'><i class=\"fa fa-save\" style=\"font-size:17px\"></i></button>";
- row[8] = "<button name='removeOverlay' data='" + id + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
+
+ var disabled = " disabled ";
+ if (loggedUser.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.LAYOUT_MANAGEMENT), self.getProject().getId())) {
+ disabled = "";
+ }
+
+
+ row[7] = "<button name='saveOverlay' data='" + id + "'" + disabled + "><i class=\"fa fa-save\" style=\"font-size:17px\"></i></button>";
+ row[8] = "<button name='removeOverlay' data='" + id + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
return row;
};
@@ -1053,7 +1068,7 @@ EditProjectDialog.prototype.openAddOverlayDialog = function () {
});
return self._addOverlayDialog.init().then(function () {
return self._addOverlayDialog.open();
- }).then(function(){
+ }).then(function () {
return self._addOverlayDialog;
});
};
diff --git a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
index e4addc6aff9b3d8cdfd8235ca57c7dc048efd752..aa5e8e492d8f4c2a799181150d19971c62de980f 100644
--- a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
@@ -346,9 +346,9 @@ MapsAdminPanel.prototype.onAddClicked = function () {
return dialog.open();
});
} else {
- dialog.clear();
- dialog.open();
- return Promise.resolve();
+ return dialog.clear().then(function () {
+ return dialog.open();
+ })
}
};
@@ -480,12 +480,9 @@ MapsAdminPanel.prototype.showEditDialog = function (id) {
return ServerConnector.getProject(id).then(function (project) {
return self.getDialog(project);
}).then(function (dialog) {
-
dialog.open();
+ }).finally(function () {
GuiConnector.hideProcessing();
- }).then(null, function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
});
};
@@ -500,11 +497,8 @@ MapsAdminPanel.prototype.showLogs = function (id, level) {
GuiConnector.showProcessing();
return self.getLogDialog(id, level).then(function (dialog) {
return dialog.open();
- }).then(function () {
- GuiConnector.hideProcessing();
- }, function (error) {
+ }).finally(function () {
GuiConnector.hideProcessing();
- return Promise.reject(error);
});
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 3ae1d5a4d8f41b3a1192f4433c47fdf2453589b7..2e3f3e6b30009722acb4ff6c8ed1c840475a702b 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -1142,6 +1142,26 @@ GuiUtils.prototype.hideTab = function (abstractGuiElement, panel) {
}
};
+/**
+ *
+ * @param {HTMLElement} element
+ * @param {string} message
+ */
+GuiUtils.prototype.disableTab = function (element, message) {
+ $(element).children().css("visibility", "hidden");
+ $("[class='minerva-help-button']", element).children().css("visibility", "visible");
+ var hideReasonDiv = document.createElement("div");
+ hideReasonDiv.className = "searchPanel";
+
+ var center = document.createElement("center");
+ var messageDiv = document.createElement("h4");
+ messageDiv.innerHTML = message;
+ center.appendChild(messageDiv);
+ hideReasonDiv.appendChild(center);
+
+ $(element).prepend(hideReasonDiv);
+};
+
/**
*
* @param {AbstractGuiElement} abstractGuiElement
diff --git a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
index b9868ad2234bc07938ef15ba0e1b449ec6990254..585b2e2f18e2c9448ab139cd19ba5fc3a8c57afc 100644
--- a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
@@ -108,7 +108,7 @@ PublicationListDialog.prototype._dataTableAjaxCall = function (data, callback) {
row[3] = article.journal;
row[4] = article.year;
} else {
- row[0] = publicationList.data[i].publication.id;
+ row[0] = publicationList.data[i].publication.resource;
row[1] = "N/A";
row[2] = "N/A";
row[3] = "N/A";
@@ -304,7 +304,7 @@ PublicationListDialog.prototype.publicationListToArray = function (publicationLi
row[3] = article.journal;
row[4] = article.year;
} else {
- row[0] = entry.publication.id;
+ row[0] = entry.publication.resource;
row[1] = "N/A";
row[2] = "N/A";
row[3] = "N/A";
diff --git a/frontend-js/src/main/js/map/data/PrivilegeType.js b/frontend-js/src/main/js/map/data/PrivilegeType.js
index a708574bab7adc6ade238472a3e6c1e28ed51f01..ba6e5ff2a42565baf75e568c55a58df43040089d 100644
--- a/frontend-js/src/main/js/map/data/PrivilegeType.js
+++ b/frontend-js/src/main/js/map/data/PrivilegeType.js
@@ -36,6 +36,7 @@ PrivilegeType.MANAGE_PLUGINS = 'MANAGE_PLUGINS';
PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
PrivilegeType.ADD_MAP = 'ADD_MAP';
PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
+PrivilegeType.LAYOUT_MANAGEMENT = 'LAYOUT_MANAGEMENT';
/**
*
diff --git a/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
index ec175e302dc7859ea7096e54cfaf37e1e7ea60d4..840128d97362b0e219442dc14fa165cca275e666 100644
--- a/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
@@ -6,7 +6,8 @@ var EditProjectDialog = require('../../../../main/js/gui/admin/EditProjectDialog
var ServerConnector = require('../../ServerConnector-mock');
var logger = require('../../logger');
-var assert = require('assert');
+var chai = require('chai');
+var assert = chai.assert;
var Promise = require('bluebird');
describe('EditProjectDialog', function () {
@@ -130,4 +131,37 @@ describe('EditProjectDialog', function () {
});
});
+ describe('overlayToTableRow', function () {
+ it('as not admin', function () {
+ var dialog;
+ helper.loginAsAdmin();
+ return createDialog().then(function (result) {
+ dialog = result;
+ return ServerConnector.getUsers();
+ }).then(function (users) {
+ helper.loginWithoutAccess();
+ var overlay = helper.createOverlay();
+ var data = dialog.overlayToTableRow(overlay, users);
+ assert.ok(data[7].indexOf("disabled") >= 0)
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+ it('as admin', function () {
+ var dialog;
+ helper.loginAsAdmin();
+ return createDialog().then(function (result) {
+ dialog = result;
+ return ServerConnector.getUsers();
+ }).then(function (users) {
+ var overlay = helper.createOverlay();
+ var data = dialog.overlayToTableRow(overlay, users);
+ assert.equal(data[7].indexOf("disabled"), -1)
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+ });
+
+
});
diff --git a/frontend-js/src/test/js/gui/admin/MapsAdminPanel-test.js b/frontend-js/src/test/js/gui/admin/MapsAdminPanel-test.js
index bb98eef61d4e8cb994e1b8d7e184b66035dc36f3..37dc06d61f4493f407e2f6fc608b77a7105a4b77 100644
--- a/frontend-js/src/test/js/gui/admin/MapsAdminPanel-test.js
+++ b/frontend-js/src/test/js/gui/admin/MapsAdminPanel-test.js
@@ -7,6 +7,7 @@ var ServerConnector = require('../../ServerConnector-mock');
var logger = require('../../logger');
var assert = require('assert');
+var Promise = require('bluebird');
function createMapsAdminPanel() {
return new MapsAdminPanel({
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index 36b05a8d4c20e84205612a4c9ca291d20a08b5a8..7d06c068c228d8125d35c359e01d065d36be4cd2 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -219,7 +219,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
minPoint.getY() + COMPARTMENT_BORDER, dimension.getWidth() - COMPARTMENT_BORDER * 2,
dimension.getHeight() - COMPARTMENT_BORDER * 2);
for (Element element : compartment.getElements()) {
- if (!elements.contains(element) && element.getBorder()!=null) {
+ if (!elements.contains(element) && element.getBorder() != null && element.getX() != 0 && element.getY() != 0) {
border.add(element.getBorder());
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 213a598b666218d20e79b42bdd847d8a22b6d8fe..ad86777a623847e843ab021e5838554406828a88 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -151,7 +151,7 @@ public interface Model {
* @param elements
* list of elements
*/
- void addElements(List<? extends Element> elements);
+ void addElements(Collection<? extends Element> elements);
/**
* Sets new short description of the model.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index b0bae9102df897f2000370b9f8349511a17a0d01..067648d9e8530634e4ee7f61f3d7327c346326ee 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -198,7 +198,7 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addElements(List<? extends Element> elements) {
+ public void addElements(Collection<? extends Element> elements) {
for (Element element : elements) {
addElement(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 23f9e1802e56b00e13e442fe9e69befc0ad3f2ad..9245aee4c29e1a95dfa1efda8921442fb420b9ff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -322,7 +322,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
* @see x
*/
public void setX(String string) {
- this.x = Double.parseDouble(string);
+ setX(Double.parseDouble(string));
}
/**
@@ -483,7 +483,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
* @return rectangle border
*/
public Rectangle2D getBorder() {
- if (x == null || y == null || width == null || height == null) {
+ if (x == null || y == null || width == null || height == null || width == 0.0 || height == 0.0) {
return null;
}
return new Rectangle2D.Double(x, y, width, height);
diff --git a/persist/src/main/resources/db/migration/V1__base.sql b/persist/src/main/resources/db/migration/V1__base.sql
index 0e8f1b24a5d754258f6963b7349ccfb252d5bd42..2315f11629ebf4eb4383f323ca55c04c11b3e78d 100644
--- a/persist/src/main/resources/db/migration/V1__base.sql
+++ b/persist/src/main/resources/db/migration/V1__base.sql
@@ -13,7 +13,6 @@ SET client_encoding = 'UTF8';
SET standard_conforming_strings = on;
SET check_function_bodies = false;
SET client_min_messages = warning;
-SET row_security = off;
--
-- TOC entry 1 (class 3079 OID 12355)
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
index f41b6ae6261905346b8845af1fe16a21fa5c64fc..0b4304a7fd86aafe051e23aa96016239185580bb 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
@@ -139,7 +139,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp
/**
* Url used for accessing Reactome RestFULL API.
*/
- private static final String REACTOME_URL = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/";
+ public static final String REACTOME_URL = "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/RESTfulWS/";
@Override
public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
index cfc792e5f612d0caad2fad0009e871be3fb2ccb6..6dc740d05a21fc8e810c6670e6b9c47bfa2f98ad 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
@@ -173,7 +173,7 @@ public class ReactomeConnectorTest extends ReactomeTestFunctions {
@Test(timeout = 15000)
public void testCachableInterfaceByParams() throws Exception {
- String url = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/listByQuery/DatabaseObjects";
+ String url = ReactomeConnector.REACTOME_URL + "listByQuery/DatabaseObjects";
String query = "identifier=2562550\n" + url;
String newRes = "hello";
try {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
index 5412d92cafa5ca788bd8e42436993a411517d073..2c51193790a348d9229da562ba4b1413212b49dc 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
@@ -53,7 +53,7 @@ public class ReactomeReferenceGeneProductParserTest extends ReactomeTestFunction
assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
assertEquals((Integer) 48895, res.getSpecies().getDbId());
- assertEquals((Integer) 11373937, res.getReferenceGenes().get(0).getDbId());
+ assertEquals((Integer) 10586616, res.getReferenceGenes().get(0).getDbId());
} catch (Exception e) {
e.printStackTrace();
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
index 1cfb460fdd0e475b183fc36a0f44ef9cf4880bc6..fc18b30ee840e7c8a35747f728832f10c14a76e2 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
@@ -39,7 +39,7 @@ public class ReactomeReferenceIsoformParserTest extends ReactomeTestFunctions {
assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
assertEquals("false", res.getIsSequenceChanged());
assertEquals((Integer) 48887, res.getSpecies().getDbId());
- assertEquals((Integer) 11373937, res.getReferenceGenes().get(0).getDbId());
+ assertEquals((Integer) 10586616, res.getReferenceGenes().get(0).getDbId());
assertEquals((Integer) 192971, res.getReferenceTranscripts().get(0).getDbId());
assertEquals((Integer) 402286, res.getIsoformParents().get(0).getDbId());
assertEquals("UniProt:P02545-1 LMNA", res.getDisplayName());
diff --git a/reactome/testFiles/reactome/referenceGeneProduct.xml b/reactome/testFiles/reactome/referenceGeneProduct.xml
index 502894eef6af22255c140af50ca417422668445a..a3458d75e34352146a9dd6b4d329e5c4dae5bddc 100644
--- a/reactome/testFiles/reactome/referenceGeneProduct.xml
+++ b/reactome/testFiles/reactome/referenceGeneProduct.xml
@@ -20,7 +20,7 @@
<schemaClass>Species</schemaClass>
</species>
<referenceGene>
- <dbId>11373937</dbId>
+ <dbId>10586616</dbId>
<displayName>BioGPS Gene:1 A1BG</displayName>
<schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene>
diff --git a/reactome/testFiles/reactome/referenceIsoform.xml b/reactome/testFiles/reactome/referenceIsoform.xml
index 8d08e978b194355ce6d27192a52b759c8a67989c..415b1bba7b619d406c2a81d0a8f83a290cf441d1 100644
--- a/reactome/testFiles/reactome/referenceIsoform.xml
+++ b/reactome/testFiles/reactome/referenceIsoform.xml
@@ -382,7 +382,7 @@
<schemaClass>Species</schemaClass>
</species>
<referenceGene>
- <dbId>11373937</dbId>
+ <dbId>10586616</dbId>
<displayName>BioGPS Gene:1 A1BG</displayName>
<schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index 7aa17f4e66616f91a793de617f2e3541d369440b..6fa4406ef870369fff71405de599215cbd5874b1 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -11,6 +11,7 @@ import java.util.Set;
import java.util.SortedMap;
import java.util.TreeMap;
+import org.apache.commons.lang3.math.NumberUtils;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@@ -21,6 +22,7 @@ import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
@@ -89,7 +91,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
this.searchService = searchService;
}
- private enum SortColumn {
+ enum SortColumn {
PUBMED_ID("pubmedId"),
YEAR("year"),
JOURNAL("journal"),
@@ -159,7 +161,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
return result;
}
- private Comparator<Entry<MiriamData, List<BioEntity>>> getComparatorForColumn(SortColumn sortColumnEnum,
+ Comparator<Entry<MiriamData, List<BioEntity>>> getComparatorForColumn(SortColumn sortColumnEnum,
String sortOrder) {
final int orderFactor;
if (sortOrder.toLowerCase().equals("desc")) {
@@ -171,13 +173,16 @@ public class PublicationsRestImpl extends BaseRestImpl {
return null;
} else if (sortColumnEnum.equals(SortColumn.PUBMED_ID)) {
return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
+ IntegerComparator integerComparator = new IntegerComparator();
+
@Override
public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
- Integer id1 = Integer.valueOf(o1.getKey().getResource());
- Integer id2 = Integer.valueOf(o2.getKey().getResource());
- return id1.compareTo(id2) * orderFactor;
+ Integer id1 = extractPubmedId(o1.getKey());
+ Integer id2 = extractPubmedId(o2.getKey());
+ return integerComparator.compare(id1, id2) * orderFactor;
}
+
};
} else if (sortColumnEnum.equals(SortColumn.YEAR)) {
return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
@@ -310,4 +315,13 @@ public class PublicationsRestImpl extends BaseRestImpl {
return pubmedParser.getPubmedArticleById(Integer.valueOf(resource));
}
+ private Integer extractPubmedId(MiriamData md) {
+ if (NumberUtils.isDigits(md.getResource())) {
+ return Integer.valueOf(md.getResource());
+ } else {
+ return null;
+ }
+
+ }
+
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
index 0cfca04523e45e92496b967c467e4f3a10a6169a..ee528a95c08a5c9b5191931731e219f29f5162ba 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
@@ -1,13 +1,18 @@
package lcsb.mapviewer.api.projects.models.publications;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
+import java.util.ArrayList;
+import java.util.Comparator;
import java.util.List;
import java.util.Map;
+import java.util.TreeMap;
+import java.util.Map.Entry;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -19,6 +24,10 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl.SortColumn;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
@@ -124,4 +133,48 @@ public class PublicationsRestImplTest extends RestTestFunctions {
return _projectRestImpl;
}
+ @Test
+ public void testComparatorForColumnWithInvalidData() {
+ Entry<MiriamData, List<BioEntity>> valid = new Entry<MiriamData, List<BioEntity>>() {
+
+ @Override
+ public List<BioEntity> setValue(List<BioEntity> value) {
+ return null;
+ }
+
+ @Override
+ public List<BioEntity> getValue() {
+ return new ArrayList<>();
+ }
+
+ @Override
+ public MiriamData getKey() {
+ return new MiriamData(MiriamType.PUBMED, "12345");
+ }
+ };
+ Entry<MiriamData, List<BioEntity>> invalid = new Entry<MiriamData, List<BioEntity>>() {
+
+ @Override
+ public List<BioEntity> setValue(List<BioEntity> value) {
+ return null;
+ }
+
+ @Override
+ public List<BioEntity> getValue() {
+ return new ArrayList<>();
+ }
+
+ @Override
+ public MiriamData getKey() {
+ return new MiriamData(MiriamType.PUBMED, "");
+ }
+ };
+ for (SortColumn sortColumn : SortColumn.values()) {
+ Comparator<Entry<MiriamData, List<BioEntity>>> comparator = _projectRestImpl.getComparatorForColumn(sortColumn,
+ "desc");
+ assertNotNull(comparator.compare(valid, invalid));
+
+ }
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 50acecfe1e036ca58799145fb5bdc73749163921..31aad6fe6743e53fc1146d45e4a31ae53ac6d216 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -1202,15 +1202,6 @@ public class ProjectService implements IProjectService {
@Override
public void updateProject(Project project, String token) throws SecurityException {
projectDao.update(project);
- if (token != null) {
- Model model = modelService.getLastModelByProjectId(project.getProjectId(), token);
- if (model != null) {
- // TODO it's a hack to prevent lazy initialization of the project
- project.getLayouts();
- project.getOverviewImages();
- model.setProject(project);
- }
- }
}
/**
diff --git a/web/src/main/webapp/index.xhtml b/web/src/main/webapp/index.xhtml
index 59e7efe6cbb829e6908fd879050ae326dc88eada..f745a7959fd0b6aaf43ed338012b9c06510b9267 100644
--- a/web/src/main/webapp/index.xhtml
+++ b/web/src/main/webapp/index.xhtml
@@ -35,6 +35,17 @@
var btn = $.fn.button.noConflict(); // reverts $.fn.button to jqueryui btn
$.fn.btn = btn; // assigns bootstrap button functionality to $.fn.btn
+ /**
+ * Safari has some issue with the jquery css or the way JSF presents the CSS resources.
+ * This is a hack that fixes this issue by forcing the icon sprite png to be loaded once the document is ready.
+ */
+ $('document').ready(function() {
+ var style = document.createElement("style");
+ var styleText = document.createTextNode(".ui-icon { background-image: url(/minerva/javax.faces.resource/images/ui-icons_616161_256x240.png.xhtml?ln=primefaces-aristo&m_version=Unknown) !important; }");
+ style.appendChild(styleText);
+ document.head.appendChild(style);
+ });
+
function initMap(){
var element = document.getElementById('minervaAppDiv');
return minerva.create({