diff --git a/frontend-js/.idea/dictionaries/piotr_gawron.xml b/frontend-js/.idea/dictionaries/piotr_gawron.xml
new file mode 100644
index 0000000000000000000000000000000000000000..efca1ca385e9a2c524561d337471a9927a616985
--- /dev/null
+++ b/frontend-js/.idea/dictionaries/piotr_gawron.xml
@@ -0,0 +1,28 @@
+<component name="ProjectDictionaryState">
+ <dictionary name="piotr.gawron">
+ <words>
+ <w>antisense</w>
+ <w>biocompendium</w>
+ <w>chebi</w>
+ <w>chembl</w>
+ <w>drugbank</w>
+ <w>ensembl</w>
+ <w>entrez</w>
+ <w>heterodimer</w>
+ <w>hgnc</w>
+ <w>hmdb</w>
+ <w>interpro</w>
+ <w>isoform</w>
+ <w>kegg</w>
+ <w>lcsb</w>
+ <w>mapviewer</w>
+ <w>omim</w>
+ <w>pubchem</w>
+ <w>pubmed</w>
+ <w>reactome</w>
+ <w>refseq</w>
+ <w>sbgn</w>
+ <w>uniprot</w>
+ </words>
+ </dictionary>
+</component>
\ No newline at end of file
diff --git a/frontend-js/.idea/workspace.xml b/frontend-js/.idea/workspace.xml
index 23e9fb403c2b6fe26a55e72865710b3eadae973f..a74db47d9d25a7972d873da6c1b1c2173761479c 100644
--- a/frontend-js/.idea/workspace.xml
+++ b/frontend-js/.idea/workspace.xml
@@ -6,7 +6,13 @@
</component>
<component name="ChangeListManager">
<list default="true" id="c119f0dd-fdda-4d02-a51e-86bc6ef7e50c" name="Default" comment="">
+ <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/.idea/dictionaries/piotr_gawron.xml" />
+ <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/src/main/js/map/data/UserPreferences.js" />
+ <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/src/test/js/map/data/UserPreferences-test.js" />
+ <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/testFiles/preferences.json" />
<change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/helper.js" afterPath="$PROJECT_DIR$/src/test/js/helper.js" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java" afterPath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java" />
</list>
<ignored path="$PROJECT_DIR$/.tmp/" />
<ignored path="$PROJECT_DIR$/temp/" />
@@ -20,102 +26,98 @@
</component>
<component name="FileEditorManager">
<leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
- <file leaf-file-name="ServerConnector.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/ServerConnector.js">
+ <file leaf-file-name="OverviewDialog.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/gui/OverviewDialog.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="15623">
- <caret line="919" column="18" lean-forward="false" selection-start-line="919" selection-start-column="18" selection-end-line="919" selection-end-column="18" />
+ <state relative-caret-position="0">
+ <caret line="195" column="65" lean-forward="false" selection-start-line="195" selection-start-column="65" selection-end-line="195" selection-end-column="65" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="SessionData.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/SessionData.js">
+ <file leaf-file-name="AbstractExportPanel.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="935">
- <caret line="55" column="17" lean-forward="false" selection-start-line="55" selection-start-column="17" selection-end-line="55" selection-end-column="17" />
+ <state relative-caret-position="153">
+ <caret line="9" column="42" lean-forward="false" selection-start-line="9" selection-start-column="42" selection-end-line="9" selection-end-column="42" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="Configuration.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/Configuration.js">
+ <file leaf-file-name="PublicationListDialog.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/gui/leftPanel/PublicationListDialog.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="697">
- <caret line="41" column="27" lean-forward="false" selection-start-line="41" selection-start-column="27" selection-end-line="41" selection-end-column="27" />
+ <state relative-caret-position="1088">
+ <caret line="64" column="48" lean-forward="false" selection-start-line="64" selection-start-column="48" selection-end-line="64" selection-end-column="48" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="Functions.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/Functions.js">
+ <file leaf-file-name="AbstractInfoWindow.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/map/window/AbstractInfoWindow.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="1190">
- <caret line="70" column="9" lean-forward="false" selection-start-line="70" selection-start-column="9" selection-end-line="70" selection-end-column="9" />
+ <state relative-caret-position="17">
+ <caret line="190" column="16" lean-forward="false" selection-start-line="190" selection-start-column="16" selection-end-line="190" selection-end-column="16" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="OverviewDialog.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/gui/OverviewDialog.js">
+ <file leaf-file-name="User.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/map/data/User.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="3315">
- <caret line="195" column="65" lean-forward="false" selection-start-line="195" selection-start-column="65" selection-end-line="195" selection-end-column="65" />
+ <state relative-caret-position="0">
+ <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="AbstractExportPanel.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js">
+ <file leaf-file-name="UserPreferences.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/map/data/UserPreferences.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="153">
- <caret line="9" column="42" lean-forward="false" selection-start-line="9" selection-start-column="42" selection-end-line="9" selection-end-column="42" />
+ <state relative-caret-position="570">
+ <caret line="48" column="0" lean-forward="false" selection-start-line="48" selection-start-column="0" selection-end-line="48" selection-end-column="0" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="PublicationListDialog.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/gui/leftPanel/PublicationListDialog.js">
+ <file leaf-file-name="assert.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/node_modules/chai/lib/chai/interface/assert.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="1088">
- <caret line="64" column="48" lean-forward="false" selection-start-line="64" selection-start-column="48" selection-end-line="64" selection-end-column="48" />
+ <state relative-caret-position="218">
+ <caret line="84" column="30" lean-forward="false" selection-start-line="84" selection-start-column="30" selection-end-line="84" selection-end-column="30" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="AbstractInfoWindow.js" pinned="false" current-in-tab="true">
- <entry file="file://$PROJECT_DIR$/src/main/js/map/window/AbstractInfoWindow.js">
+ <file leaf-file-name="UserPreferences-test.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/test/js/map/data/UserPreferences-test.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="246">
- <caret line="190" column="16" lean-forward="true" selection-start-line="190" selection-start-column="16" selection-end-line="190" selection-end-column="16" />
+ <state relative-caret-position="204">
+ <caret line="12" column="23" lean-forward="true" selection-start-line="12" selection-start-column="23" selection-end-line="12" selection-end-column="23" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="minerva.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/main/js/minerva.js">
+ <file leaf-file-name="preferences.json" pinned="false" current-in-tab="true">
+ <entry file="file://$PROJECT_DIR$/testFiles/preferences.json">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="11135">
- <caret line="655" column="28" lean-forward="false" selection-start-line="655" selection-start-column="28" selection-end-line="655" selection-end-column="28" />
- <folding>
- <marker date="1503677591650" expanded="true" signature="16592:16651" ph="..." />
- <marker date="1503677591650" expanded="true" signature="19917:19976" ph="..." />
- <marker date="1503677591650" expanded="true" signature="20784:20843" ph="..." />
- </folding>
+ <state relative-caret-position="306">
+ <caret line="18" column="6" lean-forward="true" selection-start-line="18" selection-start-column="6" selection-end-line="18" selection-end-column="6" />
+ <folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="dual-listbox.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/node_modules/dual-listbox/dist/dual-listbox.js">
+ <file leaf-file-name="Submap-test.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/test/js/map/Submap-test.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="0">
<caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
@@ -128,8 +130,6 @@
</component>
<component name="FindInProjectRecents">
<findStrings>
- <find>self =</find>
- <find>InvalidArgumentError</find>
<find>getFileContent</find>
<find>getConverter</find>
<find>chai</find>
@@ -158,6 +158,8 @@
<find>_directeEvidence</find>
<find>changedToCustimzed</find>
<find>getParamsgetParams</find>
+ <find>User</find>
+ <find>fs</find>
</findStrings>
<replaceStrings>
<replace>ValidationError</replace>
@@ -168,6 +170,7 @@
<replace>LEGEND_INDICATORS_OL</replace>
<replace>_directEvidence</replace>
<replace>changedToCustomized</replace>
+ <replace>UserPreferences</replace>
</replaceStrings>
<dirStrings>
<dir>C:\Users\piotr.gawron\workspace\MapViewer-parent\frontend-js\src\main\js\gui\leftPanel</dir>
@@ -180,9 +183,6 @@
<component name="IdeDocumentHistory">
<option name="CHANGED_PATHS">
<list>
- <option value="$PROJECT_DIR$/src/main/js/gui/leftPanel/GuiUtils.js" />
- <option value="$PROJECT_DIR$/src/main/js/gui/leftPanel/SearchPanel.js" />
- <option value="$PROJECT_DIR$/src/test/js/map/overlay/UserDbOverlay-test.js" />
<option value="$PROJECT_DIR$/src/test/js/map/overlay/DrugDbOverlay-test.js" />
<option value="$PROJECT_DIR$/src/test/js/map/data/ReferenceGenomeGeneMapping-test.js" />
<option value="$PROJECT_DIR$/src/test/js/map/data/LayoutData-test.js" />
@@ -215,7 +215,6 @@
<option value="$PROJECT_DIR$/src/test/js/ServerConnector-test.js" />
<option value="$PROJECT_DIR$/src/test/js/mocha-config.js" />
<option value="$PROJECT_DIR$/src/test/js/ServerConnector-mock.js" />
- <option value="$PROJECT_DIR$/src/test/js/helper.js" />
<option value="$PROJECT_DIR$/src/test/js/gui/LoginDialog-test.js" />
<option value="$PROJECT_DIR$/src/test/js/gui/CommentDialog-test.js" />
<option value="$PROJECT_DIR$/src/test/js/gui/leftPanel/GenericSearchPanel-test.js" />
@@ -231,6 +230,10 @@
<option value="$PROJECT_DIR$/src/test/js/map/data/IdentifiedElement-test.js" />
<option value="$PROJECT_DIR$/src/test/js/minerva-test.js" />
<option value="$PROJECT_DIR$/src/main/js/GuiConnector.js" />
+ <option value="$PROJECT_DIR$/src/test/js/helper.js" />
+ <option value="$PROJECT_DIR$/src/main/js/map/data/UserPreferences.js" />
+ <option value="$PROJECT_DIR$/src/test/js/map/data/UserPreferences-test.js" />
+ <option value="$PROJECT_DIR$/testFiles/preferences.json" />
</list>
</option>
</component>
@@ -238,6 +241,13 @@
<component name="JsBuildToolPackageJson" detection-done="true" sorting="DEFINITION_ORDER">
<package-json value="$PROJECT_DIR$/package.json" />
</component>
+ <component name="JsFlowSettings">
+ <service-enabled>true</service-enabled>
+ <exe-path />
+ <annotation-enable>false</annotation-enable>
+ <other-services-enabled>true</other-services-enabled>
+ <auto-save>true</auto-save>
+ </component>
<component name="JsGulpfileManager">
<detection-done>true</detection-done>
<sorting>DEFINITION_ORDER</sorting>
@@ -325,6 +335,11 @@
<id>XPath</id>
</State>
</expanded-state>
+ <selected-state>
+ <State>
+ <id>AngularJS</id>
+ </State>
+ </selected-state>
</profile-state>
</entry>
</component>
@@ -345,7 +360,6 @@
</navigator>
<panes>
<pane id="Scratches" />
- <pane id="Scope" />
<pane id="ProjectPane">
<subPane>
<expand>
@@ -353,10 +367,81 @@
<item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
<item name="frontend-js" type="462c0819:PsiDirectoryNode" />
</path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="main" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="main" type="462c0819:PsiDirectoryNode" />
+ <item name="js" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="main" type="462c0819:PsiDirectoryNode" />
+ <item name="js" type="462c0819:PsiDirectoryNode" />
+ <item name="map" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="main" type="462c0819:PsiDirectoryNode" />
+ <item name="js" type="462c0819:PsiDirectoryNode" />
+ <item name="map" type="462c0819:PsiDirectoryNode" />
+ <item name="data" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="test" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="test" type="462c0819:PsiDirectoryNode" />
+ <item name="js" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="test" type="462c0819:PsiDirectoryNode" />
+ <item name="js" type="462c0819:PsiDirectoryNode" />
+ <item name="map" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="src" type="462c0819:PsiDirectoryNode" />
+ <item name="test" type="462c0819:PsiDirectoryNode" />
+ <item name="js" type="462c0819:PsiDirectoryNode" />
+ <item name="map" type="462c0819:PsiDirectoryNode" />
+ <item name="data" type="462c0819:PsiDirectoryNode" />
+ </path>
+ <path>
+ <item name="frontend-js" type="b2602c69:ProjectViewProjectNode" />
+ <item name="frontend-js" type="462c0819:PsiDirectoryNode" />
+ <item name="testFiles" type="462c0819:PsiDirectoryNode" />
+ </path>
</expand>
<select />
</subPane>
</pane>
+ <pane id="Scope" />
</panes>
</component>
<component name="PropertiesComponent">
@@ -365,7 +450,7 @@
<property name="nodejs_interpreter_path" value="C:/Program Files/nodejs/node" />
<property name="HbShouldOpenHtmlAsHb" value="" />
<property name="nodejs.mocha.mocha_node_package_dir" value="$PROJECT_DIR$/node_modules/mocha" />
- <property name="settings.editor.selected.configurable" value="reference.settings.ide.settings.spelling" />
+ <property name="settings.editor.selected.configurable" value="JavaScript.Libraries" />
<property name="run.code.analysis.last.selected.profile" value="pProject Default" />
<property name="node.js.path.for.package.jscs" value="project" />
<property name="node.js.detected.package.jscs" value="true" />
@@ -379,6 +464,8 @@
</component>
<component name="RecentsManager">
<key name="CopyFile.RECENT_KEYS">
+ <recent name="C:\Users\piotr.gawron\workspace\MapViewer-parent\frontend-js\src\test\js\map\data" />
+ <recent name="C:\Users\piotr.gawron\workspace\MapViewer-parent\frontend-js\src\main\js\map\data" />
<recent name="C:\Users\piotr.gawron\workspace\MapViewer-parent\frontend-js\testFiles\apiCalls\projects\sample" />
<recent name="C:\Users\piotr.gawron\workspace\MapViewer-parent\frontend-js\src\main\js" />
<recent name="C:\Users\piotr.gawron\workspace\MapViewer-parent\frontend-js\src\test\js" />
@@ -396,21 +483,7 @@
</list>
</option>
</component>
- <component name="RunManager" selected="npm.test">
- <configuration name="AddProjectDialog" type="mocha-javascript-test-runner" factoryName="Mocha" temporary="true" nameIsGenerated="true">
- <node-interpreter>project</node-interpreter>
- <node-options />
- <working-directory>$PROJECT_DIR$</working-directory>
- <pass-parent-env>true</pass-parent-env>
- <envs />
- <ui>bdd</ui>
- <extra-mocha-options />
- <test-kind>SUITE</test-kind>
- <test-file>$PROJECT_DIR$/src/test/js/gui/admin/AddProjectDialog-test.js</test-file>
- <test-names>
- <name value="AddProjectDialog" />
- </test-names>
- </configuration>
+ <component name="RunManager" selected="Mocha.UserPreferences.constructor">
<configuration name="AddProjectDialog.js" type="NodeJSConfigurationType" factoryName="Node.js" temporary="true" path-to-node="project" path-to-js-file="AddProjectDialog.js" working-dir="$PROJECT_DIR$/src/main/js/gui/admin">
<EXTENSION ID="com.jetbrains.nodejs.remote.docker.NodeJSDockerRunConfigurationExtension">
<option name="envVars">
@@ -488,6 +561,21 @@
<name value="toggleLegend" />
</test-names>
</configuration>
+ <configuration name="UserPreferences.constructor" type="mocha-javascript-test-runner" factoryName="Mocha" temporary="true" nameIsGenerated="true">
+ <node-interpreter>project</node-interpreter>
+ <node-options />
+ <working-directory>$PROJECT_DIR$</working-directory>
+ <pass-parent-env>true</pass-parent-env>
+ <envs />
+ <ui>bdd</ui>
+ <extra-mocha-options />
+ <test-kind>TEST</test-kind>
+ <test-file>$PROJECT_DIR$/src/test/js/map/data/UserPreferences-test.js</test-file>
+ <test-names>
+ <name value="UserPreferences" />
+ <name value="constructor" />
+ </test-names>
+ </configuration>
<configuration default="true" type="mocha-javascript-test-runner" factoryName="Mocha">
<node-interpreter>project</node-interpreter>
<node-options />
@@ -605,19 +693,19 @@
<item index="1" class="java.lang.String" itemvalue="Node.js.test without coverage" />
<item index="2" class="java.lang.String" itemvalue="npm.build-deploy" />
<item index="3" class="java.lang.String" itemvalue="npm.test" />
- <item index="4" class="java.lang.String" itemvalue="Mocha.AddProjectDialog" />
- <item index="5" class="java.lang.String" itemvalue="Mocha.ServerConnector.removeProject.default" />
- <item index="6" class="java.lang.String" itemvalue="Node.js.GuiConnector.js" />
- <item index="7" class="java.lang.String" itemvalue="Node.js.AddProjectDialog.js" />
- <item index="8" class="java.lang.String" itemvalue="Mocha.TopMenu.toggleLegend" />
+ <item index="4" class="java.lang.String" itemvalue="Mocha.ServerConnector.removeProject.default" />
+ <item index="5" class="java.lang.String" itemvalue="Node.js.GuiConnector.js" />
+ <item index="6" class="java.lang.String" itemvalue="Node.js.AddProjectDialog.js" />
+ <item index="7" class="java.lang.String" itemvalue="Mocha.TopMenu.toggleLegend" />
+ <item index="8" class="java.lang.String" itemvalue="Mocha.UserPreferences.constructor" />
</list>
<recent_temporary>
<list size="5">
- <item index="0" class="java.lang.String" itemvalue="Mocha.TopMenu.toggleLegend" />
- <item index="1" class="java.lang.String" itemvalue="Mocha.ServerConnector.removeProject.default" />
- <item index="2" class="java.lang.String" itemvalue="Node.js.AddProjectDialog.js" />
- <item index="3" class="java.lang.String" itemvalue="Node.js.GuiConnector.js" />
- <item index="4" class="java.lang.String" itemvalue="Mocha.AddProjectDialog" />
+ <item index="0" class="java.lang.String" itemvalue="Mocha.UserPreferences.constructor" />
+ <item index="1" class="java.lang.String" itemvalue="Mocha.TopMenu.toggleLegend" />
+ <item index="2" class="java.lang.String" itemvalue="Mocha.ServerConnector.removeProject.default" />
+ <item index="3" class="java.lang.String" itemvalue="Node.js.AddProjectDialog.js" />
+ <item index="4" class="java.lang.String" itemvalue="Node.js.GuiConnector.js" />
</list>
</recent_temporary>
</component>
@@ -640,44 +728,45 @@
<workItem from="1503560609163" duration="22426000" />
<workItem from="1503648028157" duration="9357000" />
<workItem from="1503673204553" duration="8891000" />
- <workItem from="1503992362005" duration="19000" />
+ <workItem from="1503992362005" duration="615000" />
+ <workItem from="1504003657581" duration="4141000" />
</task>
<servers />
</component>
<component name="TestHistory">
- <history-entry file="ServerConnector_removeProject_default - 2017.08.25 at 16h 37m 49s.xml">
- <configuration name="ServerConnector.removeProject.default" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 30m 06s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="ServerConnector_removeProject_default - 2017.08.25 at 16h 41m 03s.xml">
- <configuration name="ServerConnector.removeProject.default" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 30m 37s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="ServerConnector_removeProject_default - 2017.08.25 at 16h 42m 01s.xml">
- <configuration name="ServerConnector.removeProject.default" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 30m 52s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="ServerConnector_removeProject_default - 2017.08.25 at 16h 42m 14s.xml">
- <configuration name="ServerConnector.removeProject.default" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 40m 57s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="TopMenu_toggleLegend - 2017.08.25 at 17h 52m 36s.xml">
- <configuration name="TopMenu.toggleLegend" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 42m 21s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="TopMenu_toggleLegend - 2017.08.25 at 17h 53m 16s.xml">
- <configuration name="TopMenu.toggleLegend" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 42m 45s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="TopMenu_toggleLegend - 2017.08.25 at 17h 53m 32s.xml">
- <configuration name="TopMenu.toggleLegend" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 44m 20s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="TopMenu_toggleLegend - 2017.08.25 at 17h 53m 45s.xml">
- <configuration name="TopMenu.toggleLegend" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 46m 23s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="TopMenu_toggleLegend - 2017.08.25 at 17h 55m 56s.xml">
- <configuration name="TopMenu.toggleLegend" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 13h 46m 37s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="TopMenu_toggleLegend - 2017.08.25 at 17h 56m 08s.xml">
- <configuration name="TopMenu.toggleLegend" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="UserPreferences_constructor - 2017.08.29 at 14h 03m 14s.xml">
+ <configuration name="UserPreferences.constructor" configurationId="mocha-javascript-test-runner" />
</history-entry>
</component>
<component name="TimeTrackingManager">
- <option name="totallyTimeSpent" value="45863000" />
+ <option name="totallyTimeSpent" value="50600000" />
</component>
<component name="ToolWindowManager">
<frame x="-8" y="-8" width="1936" height="1176" extended-state="6" />
@@ -687,8 +776,8 @@
<window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
<window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.5679475" sideWeight="0.33802083" order="7" side_tool="true" content_ui="tabs" />
<window_info id="Version Control" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="8" side_tool="false" content_ui="tabs" />
+ <window_info id="Run" active="true" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.33833176" sideWeight="0.49791667" order="10" side_tool="false" content_ui="tabs" x="-170" y="502" width="1920" height="493" />
<window_info id="npm" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="true" content_ui="tabs" />
- <window_info id="Run" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33833176" sideWeight="0.49791667" order="10" side_tool="false" content_ui="tabs" x="-170" y="502" width="1920" height="493" />
<window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
<window_info id="Terminal" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="9" side_tool="false" content_ui="tabs" />
<window_info id="Favorites" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="true" content_ui="tabs" />
@@ -736,48 +825,6 @@
<watches-manager />
</component>
<component name="editorHistoryManager">
- <entry file="file://$PROJECT_DIR$/src/main/js/map/data/LayoutData.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="229">
- <caret line="18" column="17" lean-forward="false" selection-start-line="18" selection-start-column="17" selection-end-line="18" selection-end-column="17" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/map/data/IdentifiedElement.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="229">
- <caret line="80" column="18" lean-forward="false" selection-start-line="80" selection-start-column="18" selection-end-line="80" selection-end-column="18" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/map/data/BioEntity.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="136">
- <caret line="8" column="22" lean-forward="false" selection-start-line="8" selection-start-column="22" selection-end-line="8" selection-end-column="22" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/map/data/MiRna.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="204">
- <caret line="12" column="0" lean-forward="true" selection-start-line="12" selection-start-column="0" selection-end-line="12" selection-end-column="0" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/map/data/LayoutAlias.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="136">
- <caret line="8" column="19" lean-forward="false" selection-start-line="8" selection-start-column="19" selection-end-line="8" selection-end-column="19" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/map/data/Chemical.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="425">
- <caret line="31" column="25" lean-forward="false" selection-start-line="31" selection-start-column="25" selection-end-line="31" selection-end-column="25" />
- </state>
- </provider>
- </entry>
<entry file="file://$PROJECT_DIR$/src/main/js/map/data/LayoutReaction.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="102">
@@ -862,13 +909,6 @@
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/src/test/js/ServerConnector-mock.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="229">
- <caret line="51" column="9" lean-forward="false" selection-start-line="51" selection-start-column="9" selection-end-line="51" selection-end-column="9" />
- </state>
- </provider>
- </entry>
<entry file="file://$PROJECT_DIR$/src/test/js/logger.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="119">
@@ -876,13 +916,6 @@
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/src/test/js/helper.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="221">
- <caret line="327" column="4" lean-forward="false" selection-start-line="327" selection-start-column="4" selection-end-line="327" selection-end-column="4" />
- </state>
- </provider>
- </entry>
<entry file="file://$PROJECT_DIR$/src/test/js/Functions-test.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="375">
@@ -1061,7 +1094,7 @@
</entry>
<entry file="file://$PROJECT_DIR$/src/main/js/Configuration.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="697">
+ <state relative-caret-position="0">
<caret line="41" column="27" lean-forward="false" selection-start-line="41" selection-start-column="27" selection-end-line="41" selection-end-column="27" />
<folding />
</state>
@@ -1077,7 +1110,7 @@
</entry>
<entry file="file://$PROJECT_DIR$/src/main/js/gui/OverviewDialog.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="3315">
+ <state relative-caret-position="0">
<caret line="195" column="65" lean-forward="false" selection-start-line="195" selection-start-column="65" selection-end-line="195" selection-end-column="65" />
<folding />
</state>
@@ -1101,8 +1134,72 @@
</entry>
<entry file="file://$PROJECT_DIR$/src/main/js/map/window/AbstractInfoWindow.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="246">
- <caret line="190" column="16" lean-forward="true" selection-start-line="190" selection-start-column="16" selection-end-line="190" selection-end-column="16" />
+ <state relative-caret-position="17">
+ <caret line="190" column="16" lean-forward="false" selection-start-line="190" selection-start-column="16" selection-end-line="190" selection-end-column="16" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/main/js/map/data/User.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="0">
+ <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/helper.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="349">
+ <caret line="383" column="16" lean-forward="true" selection-start-line="383" selection-start-column="16" selection-end-line="383" selection-end-column="16" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/ServerConnector-mock.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="439">
+ <caret line="82" column="0" lean-forward="false" selection-start-line="71" selection-start-column="0" selection-end-line="82" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/map/Submap-test.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="0">
+ <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/main/js/map/data/UserPreferences.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="570">
+ <caret line="48" column="0" lean-forward="false" selection-start-line="48" selection-start-column="0" selection-end-line="48" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/node_modules/chai/lib/chai/interface/assert.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="218">
+ <caret line="84" column="30" lean-forward="false" selection-start-line="84" selection-start-column="30" selection-end-line="84" selection-end-column="30" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/map/data/UserPreferences-test.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="204">
+ <caret line="12" column="23" lean-forward="true" selection-start-line="12" selection-start-column="23" selection-end-line="12" selection-end-column="23" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/testFiles/preferences.json">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="306">
+ <caret line="18" column="6" lean-forward="true" selection-start-line="18" selection-start-column="6" selection-end-line="18" selection-end-column="6" />
<folding />
</state>
</provider>
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
new file mode 100644
index 0000000000000000000000000000000000000000..5a2467eaa76ab190321650e56fd53c285b1001bb
--- /dev/null
+++ b/frontend-js/src/main/js/map/data/UserPreferences.js
@@ -0,0 +1,62 @@
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+function UserPreferences(javaObject) {
+ if (javaObject !== undefined) {
+ this.setProjectUpload(javaObject["project-upload"]);
+ this.setElementAnnotators(javaObject["element-annotators"]);
+ this.setElementRequiredAnnotations(javaObject["element-required-annotations"]);
+ this.setElementValidAnnotations(javaObject["element-valid-annotations"]);
+ } else {
+ this._projectUpload = {};
+ this._elementAnnotators = {};
+ this._elementRequiredAnnotations = {};
+ this._elementValidAnnotations = {};
+ }
+}
+
+UserPreferences.prototype.setProjectUpload = function (projectUpload) {
+ this._projectUpload = {
+ autoResize: projectUpload["auto-resize"],
+ validateMiriam: projectUpload["validate-miriam"],
+ annotateModel: projectUpload["annotate-model"],
+ cacheData: projectUpload["cache-data"],
+ semanticZooming: projectUpload["semantic-zooming"],
+ sbgn: projectUpload["sbgn"]
+ };
+};
+UserPreferences.prototype.getProjectUpload = function () {
+ return this._projectUpload;
+};
+UserPreferences.prototype.setElementAnnotators = function (elementAnnotators) {
+ this._elementAnnotators = elementAnnotators;
+};
+UserPreferences.prototype.getElementAnnotators = function (className) {
+ return this._elementAnnotators[className];
+};
+UserPreferences.prototype.setElementRequiredAnnotations = function (elementRequiredAnnotations) {
+ this._elementRequiredAnnotations = {};
+ for (var key in elementRequiredAnnotations) {
+ if (elementRequiredAnnotations.hasOwnProperty(key)) {
+ var data = elementRequiredAnnotations[key];
+ this._elementRequiredAnnotations[key] = {
+ requiredAtLeastOnce: data["require-at-least-one"],
+ list: data["annotation-list"]
+ };
+ }
+ }
+};
+UserPreferences.prototype.getElementRequiredAnnotations = function (className) {
+ return this._elementRequiredAnnotations[className];
+};
+UserPreferences.prototype.setElementValidAnnotations = function (elementValidAnnotations) {
+ this._elementValidAnnotations = elementValidAnnotations;
+};
+UserPreferences.prototype.getElementValidAnnotations = function (className) {
+ return this._elementValidAnnotations[className];
+};
+
+module.exports = UserPreferences;
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index 8082f7c557a6abb31fc60f5a685b0e4f733b4958..e2a1067d19908b2fb3a1f7cfed9dc4ba1153bd8c 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -25,6 +25,7 @@ var SearchDbOverlay = require("../../main/js/map/overlay/SearchDbOverlay");
var User = require("../../main/js/map/data/User");
var Cookies = require('js-cookie');
+var fs = require('fs');
var GuiConnector = require('../../main/js/GuiConnector');
@@ -36,78 +37,78 @@ function Helper(configuration) {
this.idCounter = 1000000;
}
-Helper.prototype.setConfiguration = function(configuration) {
+Helper.prototype.setConfiguration = function (configuration) {
this._configuration = configuration;
};
-Helper.prototype.getConfiguration = function() {
+Helper.prototype.getConfiguration = function () {
return this._configuration;
};
-Helper.prototype.createCommentDbOverlay = function(map) {
+Helper.prototype.createCommentDbOverlay = function (map) {
var result = new CommentDbOverlay({
- map : map,
- name : "comment",
- allowGeneralSearch : true
+ map: map,
+ name: "comment",
+ allowGeneralSearch: true
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createSearchDbOverlay = function(map) {
+Helper.prototype.createSearchDbOverlay = function (map) {
var result = new SearchDbOverlay({
- map : map,
- name : "search",
+ map: map,
+ name: "search",
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createDbOverlay = function(map) {
+Helper.prototype.createDbOverlay = function (map) {
var result = new AbstractDbOverlay({
- map : map,
- name : "search",
+ map: map,
+ name: "search",
});
- result.clear = function() {
+ result.clear = function () {
logger.debug("Clear mock");
};
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createDrugDbOverlay = function(map) {
+Helper.prototype.createDrugDbOverlay = function (map) {
var result = new DrugDbOverlay({
- map : map,
- name : "drug",
- allowGeneralSearch : true,
- allowSearchById : true,
+ map: map,
+ name: "drug",
+ allowGeneralSearch: true,
+ allowSearchById: true,
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createChemicalDbOverlay = function(map) {
+Helper.prototype.createChemicalDbOverlay = function (map) {
var result = new ChemicalDbOverlay({
- map : map,
- name : "chemical",
- allowGeneralSearch : true,
- allowSearchById : true,
+ map: map,
+ name: "chemical",
+ allowGeneralSearch: true,
+ allowSearchById: true,
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createMiRnaDbOverlay = function(map) {
+Helper.prototype.createMiRnaDbOverlay = function (map) {
var result = new MiRnaDbOverlay({
- map : map,
- name : "mirna",
- allowGeneralSearch : true,
- allowSearchById : true,
+ map: map,
+ name: "mirna",
+ allowGeneralSearch: true,
+ allowSearchById: true,
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createComment = function(element) {
+Helper.prototype.createComment = function (element) {
var elementType = "ALIAS";
var elementId = this.idCounter++;
var id = this.idCounter++;
@@ -124,25 +125,25 @@ Helper.prototype.createComment = function(element) {
}
var result = new Comment({
- elementId : elementId,
- type : elementType,
- modelId : modelId,
- icon : "icons/comment.png",
- id : id,
- pinned : true,
- coord : {
- x : 321.5,
- y : 289.0
+ elementId: elementId,
+ type: elementType,
+ modelId: modelId,
+ icon: "icons/comment.png",
+ id: id,
+ pinned: true,
+ coord: {
+ x: 321.5,
+ y: 289.0
},
- removed : false,
- title : "title fo comment: " + id,
- content : "content of the comment # " + id
+ removed: false,
+ title: "title fo comment: " + id,
+ content: "content of the comment # " + id
});
return result;
};
-Helper.prototype.createProject = function() {
+Helper.prototype.createProject = function () {
var result = new Project();
result.setProjectId("testId");
result.setId(this.idCounter++);
@@ -150,17 +151,17 @@ Helper.prototype.createProject = function() {
return result;
};
-Helper.prototype.createUser = function() {
+Helper.prototype.createUser = function () {
var result = new User({
- login : "test_login",
- id : this.idCounter++,
- name : "some name",
- surname : "surname",
+ login: "test_login",
+ id: this.idCounter++,
+ name: "some name",
+ surname: "surname",
});
return result;
};
-Helper.prototype.createAlias = function(map) {
+Helper.prototype.createAlias = function (map) {
var mapId;
if (map === undefined) {
mapId = this.idCounter++;
@@ -168,17 +169,17 @@ Helper.prototype.createAlias = function(map) {
mapId = map.getId();
}
var result = new Alias({
- idObject : this.idCounter++,
- name : "Test element",
- type : "RNA",
- modelId : mapId,
- bounds : {
- x : 10.0,
- y : 20.0,
- width : 30.0,
- height : 40.0,
+ idObject: this.idCounter++,
+ name: "Test element",
+ type: "RNA",
+ modelId: mapId,
+ bounds: {
+ x: 10.0,
+ y: 20.0,
+ width: 30.0,
+ height: 40.0,
},
- references : [],
+ references: [],
});
if (map !== undefined) {
map.getModel().addAlias(result);
@@ -186,7 +187,7 @@ Helper.prototype.createAlias = function(map) {
return result;
};
-Helper.prototype.createLayoutAlias = function(alias) {
+Helper.prototype.createLayoutAlias = function (alias) {
var id;
if (alias instanceof Alias) {
id = alias.getId();
@@ -194,17 +195,17 @@ Helper.prototype.createLayoutAlias = function(alias) {
id = this.idCounter++;
}
var result = new LayoutAlias({
- idObject : id,
- value : 0.2,
- color : {
- a : 23
+ idObject: id,
+ value: 0.2,
+ color: {
+ a: 23
},
- geneVariations : [ {} ]
+ geneVariations: [{}]
});
return result;
};
-Helper.prototype.createLayoutReaction = function(reaction) {
+Helper.prototype.createLayoutReaction = function (reaction) {
var reactionId;
if (reaction instanceof Reaction) {
reactionId = reaction.getId();
@@ -213,28 +214,28 @@ Helper.prototype.createLayoutReaction = function(reaction) {
}
var result = new LayoutReaction({
- idObject : reactionId,
- width : 3.4,
- color : {
- a : 24,
+ idObject: reactionId,
+ width: 3.4,
+ color: {
+ a: 24,
},
- reverse : true
+ reverse: true
});
return result;
};
-Helper.prototype.createIdentifiedElement = function(element) {
+Helper.prototype.createIdentifiedElement = function (element) {
if (element === undefined) {
return new IdentifiedElement({
- type : "ALIAS",
- id : this.idCounter++,
- modelId : this.idCounter++,
+ type: "ALIAS",
+ id: this.idCounter++,
+ modelId: this.idCounter++,
});
}
return new IdentifiedElement(element);
};
-Helper.prototype.createReaction = function(map) {
+Helper.prototype.createReaction = function (map) {
var mapId = null;
if (map !== undefined) {
mapId = map.getId();
@@ -242,49 +243,49 @@ Helper.prototype.createReaction = function(map) {
mapId = this.idCounter++;
}
var result = new Reaction({
- idObject : this.idCounter++,
- lines : [ {
- start : {
- x : 434.8904109589041,
- y : 85.0
+ idObject: this.idCounter++,
+ lines: [{
+ start: {
+ x: 434.8904109589041,
+ y: 85.0
},
- end : {
- x : 410.8341500923087,
- y : 104.95576185524392
+ end: {
+ x: 410.8341500923087,
+ y: 104.95576185524392
},
- type : "START"
+ type: "START"
}, {
- start : {
- x : 404.6769250286157,
- y : 110.06345991944379
+ start: {
+ x: 404.6769250286157,
+ y: 110.06345991944379
},
- end : {
- x : 380.62066416202026,
- y : 130.0192217746877
+ end: {
+ x: 380.62066416202026,
+ y: 130.0192217746877
},
- type : "END"
- } ],
- centerPoint : new google.maps.Point(0, 0),
- modelId : mapId,
- references : [],
+ type: "END"
+ }],
+ centerPoint: new google.maps.Point(0, 0),
+ modelId: mapId,
+ references: [],
});
return result;
};
-Helper.prototype.createOptions = function(project) {
+Helper.prototype.createOptions = function (project) {
if (project === undefined) {
project = this.createProject();
}
var options = {
- mapDiv : testDiv,
- element : testDiv,
- project : project,
+ mapDiv: testDiv,
+ element: testDiv,
+ project: project,
};
return options;
};
-Helper.prototype.createModel = function() {
+Helper.prototype.createModel = function () {
var result = new Model();
result.setId(this.idCounter++);
result.setTileSize(256);
@@ -293,16 +294,16 @@ Helper.prototype.createModel = function() {
result.setMaxZoom(8);
result.setMinZoom(2);
result.setCenterLatLng({
- lat : 10,
- lng : 20
+ lat: 10,
+ lng: 20
});
result.setTopLeftLatLng({
- lat : 8,
- lng : 8
+ lat: 8,
+ lng: 8
});
result.setBottomRightLatLng({
- lat : 30,
- lng : 30
+ lat: 30,
+ lng: 30
});
var layout = this.createLayout();
@@ -310,51 +311,51 @@ Helper.prototype.createModel = function() {
return result;
};
-Helper.prototype.createLayout = function() {
+Helper.prototype.createLayout = function () {
var id = this.idCounter++;
var layout = new LayoutData({
- idObject : id,
- name : "testLayout" + id,
+ idObject: id,
+ name: "testLayout" + id,
});
return layout;
};
-Helper.prototype.createGoogleMap = function() {
+Helper.prototype.createGoogleMap = function () {
var result = new google.maps.Map(testDiv, {
- center : {
- lat : -34.397,
- lng : 150.644
+ center: {
+ lat: -34.397,
+ lng: 150.644
},
- scrollwheel : false,
- zoom : 8
+ scrollwheel: false,
+ zoom: 8
});
return result;
};
-Helper.prototype.createCustomMapOptions = function(project) {
+Helper.prototype.createCustomMapOptions = function (project) {
if (project === undefined) {
project = this.createProject();
}
var result = new CustomMapOptions({
- markerOptimization : true,
- project : project,
- element : testDiv,
- mapDiv : testDiv,
- configuration : this.getConfiguration(),
+ markerOptimization: true,
+ project: project,
+ element: testDiv,
+ mapDiv: testDiv,
+ configuration: this.getConfiguration(),
});
return result;
};
-Helper.prototype.createAbstractCustomMap = function() {
+Helper.prototype.createAbstractCustomMap = function () {
var options = this.createCustomMapOptions();
var result = new AbstractCustomMap(options.getProject().getModel(), options);
return result;
};
-Helper.prototype.createCustomMap = function(project) {
+Helper.prototype.createCustomMap = function (project) {
if (project === null) {
throw new Error("Project cannot be null");
}
@@ -366,17 +367,29 @@ Helper.prototype.createCustomMap = function(project) {
/**
* Changes url but saves the cookies.
*/
-Helper.prototype.setUrl = function(url) {
+Helper.prototype.setUrl = function (url) {
var cookies = Cookies.get();
global.dom.reconfigure({
- url : url
+ url: url
});
- for ( var cookie in cookies) {
+ for (var cookie in cookies) {
Cookies.set(cookie, cookies[cookie]);
}
GuiConnector.init();
};
+Helper.prototype.readFile = function (filename) {
+ return new Promise(function (resolve, reject) {
+ fs.readFile(filename, 'utf8', function (err, content) {
+ if (err) {
+ reject(err);
+ } else {
+ resolve(content);
+ }
+ });
+ });
+};
+
Helper.EPSILON = 1e-6;
module.exports = Helper;
diff --git a/frontend-js/src/test/js/map/data/UserPreferences-test.js b/frontend-js/src/test/js/map/data/UserPreferences-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..2f9c8e86e455206c03fe93135dbd7ce5cfea3fdd
--- /dev/null
+++ b/frontend-js/src/test/js/map/data/UserPreferences-test.js
@@ -0,0 +1,30 @@
+"use strict";
+
+require("../../mocha-config")
+/* exported logger */
+
+var UserPreferences = require('../../../../main/js/map/data/UserPreferences');
+
+var logger = require('../../logger');
+
+var chai = require('chai');
+var assert = chai.assert;
+
+var fs = require('fs');
+var Promise = require('fs');
+
+describe('UserPreferences', function () {
+ it("constructor", function () {
+ return helper.readFile("testFiles/preferences.json").then(function (content) {
+ var object = new UserPreferences(JSON.parse(content));
+ assert.ok(object);
+ assert.notOk(object.getProjectUpload().autoResize);
+ assert.ok(object.getProjectUpload().cacheData);
+
+ assert.ok(object.getElementAnnotators("lcsb.mapviewer.model.map.species.Protein").length > 0);
+ assert.ok(object.getElementValidAnnotations("lcsb.mapviewer.model.map.species.Protein").length > 0);
+ assert.ok(object.getElementRequiredAnnotations("lcsb.mapviewer.model.map.species.Protein").requiredAtLeastOnce);
+ assert.ok(object.getElementRequiredAnnotations("lcsb.mapviewer.model.map.species.Protein").list.length > 0);
+ })
+ });
+});
diff --git a/frontend-js/testFiles/preferences.json b/frontend-js/testFiles/preferences.json
new file mode 100644
index 0000000000000000000000000000000000000000..5f017aff41908460c352cd9f128b38771241ae54
--- /dev/null
+++ b/frontend-js/testFiles/preferences.json
@@ -0,0 +1,753 @@
+{
+ "element-required-annotations": {
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Chemical": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "CHEBI",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Degraded": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.PathwayCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.SimpleMolecule": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "CHEBI",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.ReceptorProtein": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Gene": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.OvalCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Protein": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.BioEntity": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.GenericProtein": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.TransportReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.IonChannelProtein": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Phenotype": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Drug": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Element": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.DissociationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.SquareCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Ion": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "CHEBI",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.Reaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.RightSquareCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.TranslationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.AntisenseRna": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Complex": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Unknown": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.TruncationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.LeftSquareCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.TruncatedProtein": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.Compartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.TopSquareCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Species": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Rna": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ }
+ },
+ "element-valid-annotations": {
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Chemical": [
+ "CHEBI",
+ "HMDB",
+ "KEGG_COMPOUND",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Degraded": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.compartment.PathwayCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.SimpleMolecule": [
+ "CHEBI",
+ "HMDB",
+ "KEGG_COMPOUND",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.ReceptorProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Gene": [
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT"
+ ],
+ "lcsb.mapviewer.model.map.compartment.OvalCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Protein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.BioEntity": [
+ ],
+ "lcsb.mapviewer.model.map.species.GenericProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TransportReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.IonChannelProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Phenotype": [
+ "GO",
+ "MESH_2012",
+ "OMIM",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Drug": [
+ "CHEBI",
+ "CHEMBL_COMPOUND",
+ "DRUGBANK",
+ "HMDB",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Element": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.DissociationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.SquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Ion": [
+ "CHEBI",
+ "HMDB",
+ "KEGG_COMPOUND",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.Reaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.RightSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranslationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.AntisenseRna": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Complex": [
+ "CHEMBL_TARGET",
+ "EC",
+ "GO",
+ "INTERPRO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Unknown": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TruncationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.LeftSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.TruncatedProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.compartment.Compartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.compartment.TopSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Species": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Rna": [
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ]
+ },
+ "element-annotators": {
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Chemical": [
+ "Chebi"
+ ],
+ "lcsb.mapviewer.model.map.species.Degraded": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.PathwayCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.SimpleMolecule": [
+ "Chebi"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.ReceptorProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Gene": [
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.compartment.OvalCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Protein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.BioEntity": [
+ ],
+ "lcsb.mapviewer.model.map.species.GenericProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TransportReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.IonChannelProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Phenotype": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Drug": [
+ ],
+ "lcsb.mapviewer.model.map.species.Element": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.DissociationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.SquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Ion": [
+ "Chebi"
+ ],
+ "lcsb.mapviewer.model.map.reaction.Reaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.RightSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranslationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.AntisenseRna": [
+ ],
+ "lcsb.mapviewer.model.map.species.Complex": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Unknown": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TruncationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.LeftSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.TruncatedProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.compartment.Compartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.compartment.TopSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Species": [
+ ],
+ "lcsb.mapviewer.model.map.species.Rna": [
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction": [
+ ]
+ },
+ "project-upload": {
+ "auto-resize": false,
+ "sbgn": false,
+ "cache-data": true,
+ "semantic-zooming": false,
+ "annotate-model": false,
+ "validate-miriam": false
+ }
+}
\ No newline at end of file
diff --git a/persist/src/db/11.1.0/fix_db_20170829.sql b/persist/src/db/11.1.0/fix_db_20170829.sql
index c5d18a2ac2cca017e749cd449d76970d507c4047..43eead655e216bcbb59e7ed06b9e8befea12e27b 100644
--- a/persist/src/db/11.1.0/fix_db_20170829.sql
+++ b/persist/src/db/11.1.0/fix_db_20170829.sql
@@ -4,3 +4,10 @@ alter table user_annotation_schema_table add column autoresizemap boolean defaul
alter table user_annotation_schema_table add column cachedata boolean default true;
alter table user_annotation_schema_table add column semanticzooming boolean default false;
alter table class_required_annotation_table RENAME column requireatlestoneannotation to requireatleastoneannotation;
+
+-- rename config annotation class name
+update class_annotator_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+update class_required_annotation_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+update class_valid_annotation_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+
+
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index 0ed3cd9889fe6e0510dbe6773e1e5e8146a50b03..b3dbe1354330db2b53e19797776072ead5ffca71 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -128,7 +128,7 @@ public class UserRestImpl extends BaseRestImpl {
private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
Map<String, Object> result = new HashMap<>();
for (UserClassValidAnnotations userClassAnnotators : classValidAnnotators) {
- result.put(userClassAnnotators.getClassName(), userClassAnnotators.getValidMiriamTypes());
+ result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getValidMiriamTypes()));
}
return result;
}
@@ -158,7 +158,12 @@ public class UserRestImpl extends BaseRestImpl {
for (UserClassRequiredAnnotations requiredAnnotations : classRequiredAnnotators) {
Map<String, Object> row = new HashMap<>();
row.put("require-at-least-one", requiredAnnotations.getRequireAtLeastOneAnnotation());
- row.put("annotation-list", requiredAnnotations.getRequiredMiriamTypes());
+ List<String> miriamTypes = new ArrayList<>();
+
+ for (MiriamType mt : requiredAnnotations.getRequiredMiriamTypes()) {
+ miriamTypes.add(mt.name());
+ }
+ row.put("annotation-list", miriamTypes);
result.put(requiredAnnotations.getClassName(), row);
}
return result;
@@ -200,7 +205,7 @@ public class UserRestImpl extends BaseRestImpl {
private Map<String, Object> prepareElementAnnotators(List<UserClassAnnotators> classAnnotators) {
Map<String, Object> result = new HashMap<>();
for (UserClassAnnotators userClassAnnotators : classAnnotators) {
- result.put(userClassAnnotators.getClassName(), userClassAnnotators.getAnnotators());
+ result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getAnnotators()));
}
return result;
}