diff --git a/frontend-js/.idea/dictionaries/piotr_gawron.xml b/frontend-js/.idea/dictionaries/piotr_gawron.xml
index e16724fb120576f533b3ba793d1ae9d326fc3728..82a73e70bcd41d5649a9df121b6afa8a010e9b1b 100644
--- a/frontend-js/.idea/dictionaries/piotr_gawron.xml
+++ b/frontend-js/.idea/dictionaries/piotr_gawron.xml
@@ -3,6 +3,7 @@
<words>
<w>antisense</w>
<w>biocompendium</w>
+ <w>celldesigner</w>
<w>chebi</w>
<w>chembl</w>
<w>drugbank</w>
@@ -16,15 +17,20 @@
<w>kegg</w>
<w>lcsb</w>
<w>mapviewer</w>
+ <w>ncbigene</w>
<w>omim</w>
<w>pubchem</w>
<w>pubmed</w>
<w>reactome</w>
<w>refseq</w>
+ <w>saccharomyces</w>
<w>sbgn</w>
+ <w>smtp</w>
<w>submap</w>
<w>submaps</w>
+ <w>toxicogenomic</w>
<w>uniprot</w>
+ <w>wikipathways</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 ee3a8ac97ad4169cb45b7396482bacc67b59449e..1456e2a7dbc1d558ccbabba7e05a777ac2866bb6 100644
--- a/frontend-js/.idea/workspace.xml
+++ b/frontend-js/.idea/workspace.xml
@@ -6,22 +6,27 @@
</component>
<component name="ChangeListManager">
<list default="true" id="c119f0dd-fdda-4d02-a51e-86bc6ef7e50c" name="Default" comment="">
- <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/.idea/webResources.xml" />
- <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/testFiles/apiCalls/users/admin.updatePreferences/PATCH_preferences.project-upload.cache-data=false&" />
- <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/testFiles/apiCalls/users/admin.updatePreferences/PATCH_preferences.project-upload.cache-data=true&" />
+ <change type="MOVED" beforePath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,icon,removed&token=MOCK_TOKEN_ID&" afterPath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,removed,type&token=MOCK_TOKEN_ID&" />
+ <change type="MOVED" beforePath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,icon,removed,pinned&token=MOCK_TOKEN_ID&" afterPath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&" />
+ <change type="MOVED" beforePath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,removed,pinned,author,email&token=MOCK_TOKEN_ID&" afterPath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/comments/models/all/columns=author,elementId,email,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&" />
+ <change type="MOVED" beforePath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID&" afterPath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Antisense RNA,Compartment,Complex,Degraded,Drug,Gene,Ion,Phenotype,Protein,RNA,Simple molecule,Unknown&token=MOCK_TOKEN_ID&" />
+ <change type="MOVED" beforePath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID&" afterPath="$PROJECT_DIR$/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Antisense RNA,Compartment,Complex,Degraded,Drug,Gene,Ion,Phenotype,Protein,RNA,Simple molecule,Unknown&token=MOCK_TOKEN_ID&" />
<change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/dictionaries/piotr_gawron.xml" afterPath="$PROJECT_DIR$/.idea/dictionaries/piotr_gawron.xml" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/frontend-js.iml" afterPath="$PROJECT_DIR$/.idea/frontend-js.iml" />
<change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/main/js/Configuration.js" afterPath="$PROJECT_DIR$/src/main/js/Configuration.js" />
<change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/main/js/ServerConnector.js" afterPath="$PROJECT_DIR$/src/main/js/ServerConnector.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/main/js/gui/admin/AddProjectDialog.js" afterPath="$PROJECT_DIR$/src/main/js/gui/admin/AddProjectDialog.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/main/js/map/data/User.js" afterPath="$PROJECT_DIR$/src/main/js/map/data/User.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/main/js/map/data/UserPreferences.js" afterPath="$PROJECT_DIR$/src/main/js/map/data/UserPreferences.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/GuiConnector-mock.js" afterPath="$PROJECT_DIR$/src/test/js/GuiConnector-mock.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/gui/Header-test.js" afterPath="$PROJECT_DIR$/src/test/js/gui/Header-test.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/gui/admin/AddProjectDialog-test.js" afterPath="$PROJECT_DIR$/src/test/js/gui/admin/AddProjectDialog-test.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/gui/admin/EditProjectDialog-test.js" afterPath="$PROJECT_DIR$/src/test/js/gui/admin/EditProjectDialog-test.js" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/map/Submap-test.js" afterPath="$PROJECT_DIR$/src/test/js/map/Submap-test.js" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js" afterPath="$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/main/js/minerva.js" afterPath="$PROJECT_DIR$/src/main/js/minerva.js" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/gui/export/ElementExportPanel-test.js" afterPath="$PROJECT_DIR$/src/test/js/gui/export/ElementExportPanel-test.js" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/gui/export/NetworkExportPanel-test.js" afterPath="$PROJECT_DIR$/src/test/js/gui/export/NetworkExportPanel-test.js" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/src/test/js/minerva-test.js" afterPath="$PROJECT_DIR$/src/test/js/minerva-test.js" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&" afterPath="$PROJECT_DIR$/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/../model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java" afterPath="$PROJECT_DIR$/../model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java" afterPath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java" afterPath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java" />
<change type="MODIFICATION" beforePath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java" afterPath="$PROJECT_DIR$/../rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/../rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java" afterPath="$PROJECT_DIR$/../rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java" />
+ <change type="MODIFICATION" beforePath="$PROJECT_DIR$/../web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java" afterPath="$PROJECT_DIR$/../web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java" />
</list>
<ignored path="$PROJECT_DIR$/.tmp/" />
<ignored path="$PROJECT_DIR$/temp/" />
@@ -35,41 +40,105 @@
</component>
<component name="FileEditorManager">
<leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
- <file leaf-file-name="AddProjectDialog-test.js" pinned="false" current-in-tab="true">
+ <file leaf-file-name="ServerConnector.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/ServerConnector.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="720">
+ <caret line="849" column="18" lean-forward="false" selection-start-line="849" selection-start-column="18" selection-end-line="849" selection-end-column="18" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ </file>
+ <file leaf-file-name="NetworkExportPanel-test.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/test/js/gui/export/NetworkExportPanel-test.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="85">
+ <caret line="5" column="0" lean-forward="false" selection-start-line="5" selection-start-column="0" selection-end-line="5" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ </file>
+ <file leaf-file-name="NetworkExportPanel.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/gui/export/NetworkExportPanel.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="98">
+ <caret line="162" column="23" lean-forward="false" selection-start-line="162" selection-start-column="23" selection-end-line="162" selection-end-column="23" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ </file>
+ <file leaf-file-name="AddProjectDialog-test.js" pinned="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/src/test/js/gui/admin/AddProjectDialog-test.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="507">
- <caret line="52" column="43" lean-forward="true" selection-start-line="52" selection-start-column="43" selection-end-line="52" selection-end-column="43" />
+ <state relative-caret-position="85">
+ <caret line="5" column="0" lean-forward="false" selection-start-line="4" selection-start-column="0" selection-end-line="5" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ </file>
+ <file leaf-file-name="AbstractExportPanel.js" pinned="false" current-in-tab="true">
+ <entry file="file://$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="234">
+ <caret line="97" column="5" lean-forward="true" selection-start-line="97" selection-start-column="5" selection-end-line="97" selection-end-column="5" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="EditProjectDialog-test.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/test/js/gui/admin/EditProjectDialog-test.js">
+ <file leaf-file-name="ElementExportPanel-test.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/test/js/gui/export/ElementExportPanel-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" />
+ <state relative-caret-position="234">
+ <caret line="31" column="39" lean-forward="false" selection-start-line="31" selection-start-column="39" selection-end-line="31" selection-end-column="39" />
<folding />
</state>
</provider>
</entry>
</file>
- <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">
+ <file leaf-file-name="Configuration.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/main/js/Configuration.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="221">
- <caret line="34" column="0" lean-forward="false" selection-start-line="34" selection-start-column="0" selection-end-line="34" selection-end-column="0" />
+ <state relative-caret-position="362">
+ <caret line="93" column="16" lean-forward="false" selection-start-line="93" selection-start-column="16" selection-end-line="93" selection-end-column="16" />
<folding />
</state>
</provider>
</entry>
</file>
- <file leaf-file-name="AddOverlayDialog-test.js" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/src/test/js/gui/AddOverlayDialog-test.js">
+ <file leaf-file-name="ServerConnector-mock.js" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/src/test/js/ServerConnector-mock.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" />
+ <state relative-caret-position="720">
+ <caret line="76" column="28" lean-forward="false" selection-start-line="71" selection-start-column="0" selection-end-line="82" selection-end-column="0" />
+ <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">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="243">
+ <caret line="338" column="65" lean-forward="false" selection-start-line="338" selection-start-column="65" selection-end-line="338" selection-end-column="65" />
+ <folding>
+ <marker date="1504026137494" expanded="true" signature="16593:16652" ph="..." />
+ <marker date="1504026137494" expanded="true" signature="19918:19977" ph="..." />
+ <marker date="1504026137494" expanded="true" signature="20785:20844" ph="..." />
+ </folding>
+ </state>
+ </provider>
+ </entry>
+ </file>
+ <file leaf-file-name="token=MOCK_TOKEN_ID&" pinned="false" current-in-tab="false">
+ <entry file="file://$PROJECT_DIR$/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="-583">
+ <caret line="0" column="10147" lean-forward="false" selection-start-line="0" selection-start-column="10147" selection-end-line="0" selection-end-column="10147" />
<folding />
</state>
</provider>
@@ -79,10 +148,6 @@
</component>
<component name="FindInProjectRecents">
<findStrings>
- <find>LEGEND_INDICATIORS_OL</find>
- <find>elemnts</find>
- <find>creatMapOptions</find>
- <find>_directeEvidence</find>
<find>changedToCustimzed</find>
<find>getParamsgetParams</find>
<find>User</find>
@@ -109,6 +174,10 @@
<find>getUpdateUserPrivilegesUrl</find>
<find>update</find>
<find>prefere</find>
+ <find>seri</find>
+ <find>Arra</find>
+ <find>TypeNa</find>
+ <find>value</find>
</findStrings>
<replaceStrings>
<replace>ValidationError</replace>
@@ -132,12 +201,6 @@
<component name="IdeDocumentHistory">
<option name="CHANGED_PATHS">
<list>
- <option value="$PROJECT_DIR$/src/main/js/gui/leftPanel/ChemicalPanel.js" />
- <option value="$PROJECT_DIR$/src/main/js/map/CustomMap.js" />
- <option value="$PROJECT_DIR$/src/main/js/map/AbstractCustomMap.js" />
- <option value="$PROJECT_DIR$/src/main/js/map/Submap.js" />
- <option value="$PROJECT_DIR$/src/main/js/map/data/Alias.js" />
- <option value="$PROJECT_DIR$/src/main/js/map/data/Reaction.js" />
<option value="$PROJECT_DIR$/src/main/js/map/data/LayoutData.js" />
<option value="$PROJECT_DIR$/src/main/js/map/data/IdentifiedElement.js" />
<option value="$PROJECT_DIR$/src/main/js/map/data/BioEntity.js" />
@@ -167,7 +230,6 @@
<option value="$PROJECT_DIR$/src/test/js/map/AbstractCustomMap-test.js" />
<option value="$PROJECT_DIR$/src/test/js/map/CustomMap-test.js" />
<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/test/js/map/data/UserPreferences-test.js" />
@@ -180,9 +242,16 @@
<option value="$PROJECT_DIR$/src/main/js/gui/admin/AddProjectDialog.js" />
<option value="$PROJECT_DIR$/src/test/js/GuiConnector-mock.js" />
<option value="$PROJECT_DIR$/src/main/js/map/data/UserPreferences.js" />
- <option value="$PROJECT_DIR$/src/main/js/ServerConnector.js" />
<option value="$PROJECT_DIR$/testFiles/apiCalls/users/admin.updatePreferences/PATCH_preferences.project-upload.cache-data=true&" />
<option value="$PROJECT_DIR$/testFiles/apiCalls/users/admin.updatePreferences/PATCH_preferences.project-upload.cache-data=false&" />
+ <option value="$PROJECT_DIR$/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&" />
+ <option value="$PROJECT_DIR$/src/test/js/minerva-test.js" />
+ <option value="$PROJECT_DIR$/src/main/js/minerva.js" />
+ <option value="$PROJECT_DIR$/src/main/js/Configuration.js" />
+ <option value="$PROJECT_DIR$/src/main/js/ServerConnector.js" />
+ <option value="$PROJECT_DIR$/src/test/js/gui/export/NetworkExportPanel-test.js" />
+ <option value="$PROJECT_DIR$/src/test/js/gui/export/ElementExportPanel-test.js" />
+ <option value="$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js" />
</list>
</option>
</component>
@@ -379,31 +448,81 @@
<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="testFiles" 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" />
+ <item name="apiCalls" 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" />
+ <item name="apiCalls" type="462c0819:PsiDirectoryNode" />
+ <item name="configuration" 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" />
+ <item name="apiCalls" type="462c0819:PsiDirectoryNode" />
+ <item name="projects" 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" />
+ <item name="apiCalls" type="462c0819:PsiDirectoryNode" />
+ <item name="projects" type="462c0819:PsiDirectoryNode" />
+ <item name="sample" 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" />
<item name="apiCalls" type="462c0819:PsiDirectoryNode" />
+ <item name="projects" type="462c0819:PsiDirectoryNode" />
+ <item name="sample" type="462c0819:PsiDirectoryNode" />
+ <item name="comments" 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" />
<item name="apiCalls" type="462c0819:PsiDirectoryNode" />
- <item name="users" type="462c0819:PsiDirectoryNode" />
+ <item name="projects" type="462c0819:PsiDirectoryNode" />
+ <item name="sample" type="462c0819:PsiDirectoryNode" />
+ <item name="comments" type="462c0819:PsiDirectoryNode" />
+ <item name="models" 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" />
<item name="apiCalls" type="462c0819:PsiDirectoryNode" />
- <item name="users" type="462c0819:PsiDirectoryNode" />
- <item name="admin.updatePreferences" type="462c0819:PsiDirectoryNode" />
+ <item name="projects" type="462c0819:PsiDirectoryNode" />
+ <item name="sample" type="462c0819:PsiDirectoryNode" />
+ <item name="comments" type="462c0819:PsiDirectoryNode" />
+ <item name="models" type="462c0819:PsiDirectoryNode" />
+ <item name="all" type="462c0819:PsiDirectoryNode" />
</path>
</expand>
<select />
@@ -451,7 +570,7 @@
</list>
</option>
</component>
- <component name="RunManager" selected="Mocha.AddProjectDialog.onUserPreferencesChange">
+ <component name="RunManager" selected="npm.build-deploy">
<configuration name="AddProjectDialog.onUserPreferencesChange" type="mocha-javascript-test-runner" factoryName="Mocha" temporary="true" nameIsGenerated="true">
<node-interpreter>project</node-interpreter>
<node-options />
@@ -467,37 +586,6 @@
<name value="onUserPreferencesChange" />
</test-names>
</configuration>
- <configuration name="ServerConnector.removeProject.default" 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/ServerConnector-test.js</test-file>
- <test-names>
- <name value="ServerConnector" />
- <name value="removeProject" />
- <name value="default" />
- </test-names>
- </configuration>
- <configuration name="TopMenu.toggleLegend" 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/gui/topMenu/TopMenu-test.js</test-file>
- <test-names>
- <name value="TopMenu" />
- <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 />
@@ -566,6 +654,21 @@
<node-interpreter value="project" />
<envs />
</configuration>
+ <configuration name="minerva global.getAllBioEntities" 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/minerva-test.js</test-file>
+ <test-names>
+ <name value="minerva global" />
+ <name value="getAllBioEntities" />
+ </test-names>
+ </configuration>
<configuration name="profile without coverage" type="NodeJSConfigurationType" factoryName="Node.js" path-to-node="project" path-to-js-file="node_modules/mocha/bin/_mocha" application-parameters="--recursive src/test" working-dir="$PROJECT_DIR$">
<profiling do-profile="true" />
<EXTENSION ID="com.jetbrains.nodejs.remote.docker.NodeJSDockerRunConfigurationExtension">
@@ -604,6 +707,17 @@
<test-kind>TEST_FILE</test-kind>
<test-file>$PROJECT_DIR$/src/test/js/gui/admin/AddProjectDialog-test.js</test-file>
</configuration>
+ <configuration name="src\test\js\gui\export\NetworkExportPanel-test.js" 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_FILE</test-kind>
+ <test-file>$PROJECT_DIR$/src/test/js/gui/export/NetworkExportPanel-test.js</test-file>
+ </configuration>
<configuration name="test without coverage" type="NodeJSConfigurationType" factoryName="Node.js" path-to-node="project" path-to-js-file="node_modules/mocha/bin/_mocha" application-parameters="--recursive src/test" working-dir="$PROJECT_DIR$">
<EXTENSION ID="com.jetbrains.nodejs.remote.docker.NodeJSDockerRunConfigurationExtension">
<option name="envVars">
@@ -641,19 +755,19 @@
<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.ServerConnector.removeProject.default" />
- <item index="5" class="java.lang.String" itemvalue="Mocha.TopMenu.toggleLegend" />
- <item index="6" class="java.lang.String" itemvalue="Mocha.UserPreferences.constructor" />
- <item index="7" class="java.lang.String" itemvalue="Mocha.src\test\js\gui\admin\AddProjectDialog-test.js" />
- <item index="8" class="java.lang.String" itemvalue="Mocha.AddProjectDialog.onUserPreferencesChange" />
+ <item index="4" class="java.lang.String" itemvalue="Mocha.UserPreferences.constructor" />
+ <item index="5" class="java.lang.String" itemvalue="Mocha.src\test\js\gui\admin\AddProjectDialog-test.js" />
+ <item index="6" class="java.lang.String" itemvalue="Mocha.AddProjectDialog.onUserPreferencesChange" />
+ <item index="7" class="java.lang.String" itemvalue="Mocha.minerva global.getAllBioEntities" />
+ <item index="8" class="java.lang.String" itemvalue="Mocha.src\test\js\gui\export\NetworkExportPanel-test.js" />
</list>
<recent_temporary>
<list size="5">
- <item index="0" class="java.lang.String" itemvalue="Mocha.AddProjectDialog.onUserPreferencesChange" />
- <item index="1" class="java.lang.String" itemvalue="Mocha.src\test\js\gui\admin\AddProjectDialog-test.js" />
- <item index="2" class="java.lang.String" itemvalue="Mocha.UserPreferences.constructor" />
- <item index="3" class="java.lang.String" itemvalue="Mocha.TopMenu.toggleLegend" />
- <item index="4" class="java.lang.String" itemvalue="Mocha.ServerConnector.removeProject.default" />
+ <item index="0" class="java.lang.String" itemvalue="Mocha.src\test\js\gui\export\NetworkExportPanel-test.js" />
+ <item index="1" class="java.lang.String" itemvalue="Mocha.minerva global.getAllBioEntities" />
+ <item index="2" class="java.lang.String" itemvalue="Mocha.AddProjectDialog.onUserPreferencesChange" />
+ <item index="3" class="java.lang.String" itemvalue="Mocha.src\test\js\gui\admin\AddProjectDialog-test.js" />
+ <item index="4" class="java.lang.String" itemvalue="Mocha.UserPreferences.constructor" />
</list>
</recent_temporary>
</component>
@@ -677,54 +791,54 @@
<workItem from="1503648028157" duration="9357000" />
<workItem from="1503673204553" duration="8891000" />
<workItem from="1503992362005" duration="615000" />
- <workItem from="1504003657581" duration="11648000" />
+ <workItem from="1504003657581" duration="14917000" />
</task>
<servers />
</component>
<component name="TestHistory">
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 17h 49m 47s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 09m 18s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 17h 50m 08s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 10m 18s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 17h 55m 59s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 11m 53s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 18h 06m 22s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 12m 11s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 18h 09m 50s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 17m 50s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 18h 12m 14s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 21m 45s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 18h 23m 26s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 24m 13s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 18h 25m 48s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="minerva_global_getAllBioEntities - 2017.08.29 at 19h 24m 41s.xml">
+ <configuration name="minerva global.getAllBioEntities" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 18h 27m 32s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="src_test_js_gui_export_NetworkExportPanel-test_js - 2017.08.29 at 19h 32m 50s.xml">
+ <configuration name="src\test\js\gui\export\NetworkExportPanel-test.js" configurationId="mocha-javascript-test-runner" />
</history-entry>
- <history-entry file="AddProjectDialog_onUserPreferencesChange - 2017.08.29 at 18h 28m 06s.xml">
- <configuration name="AddProjectDialog.onUserPreferencesChange" configurationId="mocha-javascript-test-runner" />
+ <history-entry file="src_test_js_gui_export_NetworkExportPanel-test_js - 2017.08.29 at 19h 34m 04s.xml">
+ <configuration name="src\test\js\gui\export\NetworkExportPanel-test.js" configurationId="mocha-javascript-test-runner" />
</history-entry>
</component>
<component name="TimeTrackingManager">
- <option name="totallyTimeSpent" value="58107000" />
+ <option name="totallyTimeSpent" value="61376000" />
</component>
<component name="ToolWindowManager">
<frame x="-8" y="-8" width="1936" height="1176" extended-state="6" />
<editor active="true" />
<layout>
- <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.18020834" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
+ <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.20364584" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
<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="false" 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="Run" active="true" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.24554826" 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="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" />
@@ -773,41 +887,6 @@
<watches-manager />
</component>
<component name="editorHistoryManager">
- <entry file="file://$PROJECT_DIR$/src/test/js/logger.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="119">
- <caret line="7" column="2" lean-forward="false" selection-start-line="7" selection-start-column="2" selection-end-line="7" selection-end-column="2" />
- </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">
- <caret line="238" column="19" lean-forward="false" selection-start-line="238" selection-start-column="19" selection-end-line="238" selection-end-column="19" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/test/js/gui/leftPanel/GenericSearchPanel-test.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="323">
- <caret line="111" column="27" lean-forward="false" selection-start-line="111" selection-start-column="27" selection-end-line="111" selection-end-column="27" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/test/js/gui/leftPanel/MiRnaPanel-test.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="272">
- <caret line="37" column="33" lean-forward="false" selection-start-line="37" selection-start-column="33" selection-end-line="37" selection-end-column="33" />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/src/test/js/gui/leftPanel/SubmapPanel-test.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="204">
- <caret line="12" column="10" lean-forward="false" selection-start-line="12" selection-start-column="10" selection-end-line="12" selection-end-column="10" />
- </state>
- </provider>
- </entry>
<entry file="file://$PROJECT_DIR$/src/test/js/gui/leftPanel/PublicationListDialog-test.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="204">
@@ -878,13 +957,6 @@
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/src/test/js/minerva-test.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="297">
- <caret line="22" column="0" lean-forward="false" selection-start-line="22" selection-start-column="0" selection-end-line="22" selection-end-column="0" />
- </state>
- </provider>
- </entry>
<entry file="file://$PROJECT_DIR$/src/main/js/map/marker/AbstractMarker.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="467">
@@ -907,18 +979,6 @@
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/minerva.js">
- <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>
- </provider>
- </entry>
<entry file="file://$PROJECT_DIR$/src/main/js/SessionData.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="935">
@@ -927,14 +987,6 @@
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/Configuration.js">
- <provider selected="true" editor-type-id="text-editor">
- <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>
- </provider>
- </entry>
<entry file="file://$PROJECT_DIR$/src/main/js/Functions.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="1190">
@@ -983,14 +1035,6 @@
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="17">
- <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>
<entry file="file://$PROJECT_DIR$/src/main/js/gui/OverviewDialog.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="0">
@@ -1031,14 +1075,6 @@
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/src/test/js/gui/AddOverlayDialog-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/test/js/gui/LoginDialog-test.js">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="102">
@@ -1103,22 +1139,6 @@
</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="774">
- <caret line="76" column="28" 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/main/js/ServerConnector.js">
- <provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="269">
- <caret line="849" column="18" lean-forward="true" selection-start-line="849" selection-start-column="18" selection-end-line="849" selection-end-column="18" />
- <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="536">
@@ -1162,10 +1182,110 @@
</state>
</provider>
</entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/mocha-config.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/minerva-test.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="34">
+ <caret line="2" column="23" lean-forward="false" selection-start-line="2" selection-start-column="23" selection-end-line="2" selection-end-column="23" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/gui/AddOverlayDialog-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/ServerConnector.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="720">
+ <caret line="849" column="18" lean-forward="false" selection-start-line="849" selection-start-column="18" selection-end-line="849" selection-end-column="18" />
+ <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="720">
+ <caret line="76" column="28" 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/main/js/Configuration.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="362">
+ <caret line="93" column="16" lean-forward="false" selection-start-line="93" selection-start-column="16" selection-end-line="93" selection-end-column="16" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="-583">
+ <caret line="0" column="10147" lean-forward="false" selection-start-line="0" selection-start-column="10147" selection-end-line="0" selection-end-column="10147" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/main/js/minerva.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="243">
+ <caret line="338" column="65" lean-forward="false" selection-start-line="338" selection-start-column="65" selection-end-line="338" selection-end-column="65" />
+ <folding>
+ <marker date="1504026137494" expanded="true" signature="16593:16652" ph="..." />
+ <marker date="1504026137494" expanded="true" signature="19918:19977" ph="..." />
+ <marker date="1504026137494" expanded="true" signature="20785:20844" ph="..." />
+ </folding>
+ </state>
+ </provider>
+ </entry>
<entry file="file://$PROJECT_DIR$/src/test/js/gui/admin/AddProjectDialog-test.js">
<provider selected="true" editor-type-id="text-editor">
- <state relative-caret-position="507">
- <caret line="52" column="43" lean-forward="true" selection-start-line="52" selection-start-column="43" selection-end-line="52" selection-end-column="43" />
+ <state relative-caret-position="85">
+ <caret line="5" column="0" lean-forward="false" selection-start-line="4" selection-start-column="0" selection-end-line="5" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/gui/export/NetworkExportPanel-test.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="85">
+ <caret line="5" column="0" lean-forward="false" selection-start-line="5" selection-start-column="0" selection-end-line="5" selection-end-column="0" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/main/js/gui/export/NetworkExportPanel.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="98">
+ <caret line="162" column="23" lean-forward="false" selection-start-line="162" selection-start-column="23" selection-end-line="162" selection-end-column="23" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/test/js/gui/export/ElementExportPanel-test.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="234">
+ <caret line="31" column="39" lean-forward="false" selection-start-line="31" selection-start-column="39" selection-end-line="31" selection-end-column="39" />
+ <folding />
+ </state>
+ </provider>
+ </entry>
+ <entry file="file://$PROJECT_DIR$/src/main/js/gui/export/AbstractExportPanel.js">
+ <provider selected="true" editor-type-id="text-editor">
+ <state relative-caret-position="234">
+ <caret line="97" column="5" lean-forward="true" selection-start-line="97" selection-start-column="5" selection-end-line="97" selection-end-column="5" />
<folding />
</state>
</provider>
diff --git a/frontend-js/src/main/js/Configuration.js b/frontend-js/src/main/js/Configuration.js
index d5d7899ec4a5e39682ae9698bb61bee0331b962f..549b444600c192ca59ed1402cdef2c34be59ac36 100644
--- a/frontend-js/src/main/js/Configuration.js
+++ b/frontend-js/src/main/js/Configuration.js
@@ -52,51 +52,58 @@ function Configuration(json) {
self.setPrivilegeTypes(json.privilegeTypes);
}
-Configuration.prototype.setOption = function(type, value) {
+Configuration.prototype.setOption = function (type, value) {
this._options[type] = value;
};
-Configuration.prototype.getOption = function(type) {
+Configuration.prototype.getOption = function (type) {
return this._options[type];
};
-Configuration.prototype.setOverlayTypes = function(overlayTypes) {
+Configuration.prototype.setOverlayTypes = function (overlayTypes) {
this._overlayTypes = overlayTypes;
};
-Configuration.prototype.getOverlayTypes = function() {
+Configuration.prototype.getOverlayTypes = function () {
return this._overlayTypes;
};
-Configuration.prototype.setImageConverters = function(imageConverters) {
+Configuration.prototype.setImageConverters = function (imageConverters) {
this._imageConverters = imageConverters;
};
-Configuration.prototype.getImageConverters = function() {
+Configuration.prototype.getImageConverters = function () {
return this._imageConverters;
};
-Configuration.prototype.setModelConverters = function(modelConverters) {
+Configuration.prototype.setModelConverters = function (modelConverters) {
this._modelConverters = modelConverters;
};
-Configuration.prototype.getModelConverters = function() {
+Configuration.prototype.getModelConverters = function () {
return this._modelConverters;
};
-Configuration.prototype.setElementTypes = function(elementTypes) {
+Configuration.prototype.setElementTypes = function (elementTypes) {
this._elementTypes = elementTypes;
};
-Configuration.prototype.getElementTypes = function() {
+Configuration.prototype.getElementTypes = function () {
return this._elementTypes;
};
+Configuration.prototype.getElementTypeNames = function () {
+ var result = [];
+ for (var i = 0; i < this._elementTypes.length; i++) {
+ result.push(this._elementTypes[i].name);
+ }
+ return result;
+};
-Configuration.prototype.setReactionTypes = function(reactionTypes) {
+Configuration.prototype.setReactionTypes = function (reactionTypes) {
this._reactionTypes = reactionTypes;
};
-Configuration.prototype.getReactionTypes = function() {
+Configuration.prototype.getReactionTypes = function () {
return this._reactionTypes;
};
-Configuration.prototype.setMiriamTypes = function(miriamTypes) {
+Configuration.prototype.setMiriamTypes = function (miriamTypes) {
this._miriamTypes = [];
- for ( var key in miriamTypes) {
+ for (var key in miriamTypes) {
if (miriamTypes.hasOwnProperty(key)) {
var typeData = miriamTypes[key];
this._miriamTypes.push(new MiriamType(typeData, key));
@@ -104,9 +111,9 @@ Configuration.prototype.setMiriamTypes = function(miriamTypes) {
}
};
-Configuration.prototype.setPrivilegeTypes = function(privilegeTypes) {
+Configuration.prototype.setPrivilegeTypes = function (privilegeTypes) {
this._privilegeTypes = [];
- for ( var key in privilegeTypes) {
+ for (var key in privilegeTypes) {
if (privilegeTypes.hasOwnProperty(key)) {
var typeData = privilegeTypes[key];
this._privilegeTypes.push(new PrivilegeType(typeData, key));
@@ -114,11 +121,11 @@ Configuration.prototype.setPrivilegeTypes = function(privilegeTypes) {
}
};
-Configuration.prototype.getPrivilegeTypes = function() {
+Configuration.prototype.getPrivilegeTypes = function () {
return this._privilegeTypes;
};
-Configuration.prototype.getMiriamTypeByName = function(name) {
+Configuration.prototype.getMiriamTypeByName = function (name) {
var self = this;
for (var i = 0; i < self._miriamTypes.length; i++) {
var miriamType = self._miriamTypes[i];
@@ -129,16 +136,16 @@ Configuration.prototype.getMiriamTypeByName = function(name) {
return null;
};
-Configuration.prototype.setModificationStateTypes = function(modificationStateTypes) {
+Configuration.prototype.setModificationStateTypes = function (modificationStateTypes) {
this._modificationStateTypes = [];
- for ( var key in modificationStateTypes) {
+ for (var key in modificationStateTypes) {
if (modificationStateTypes.hasOwnProperty(key)) {
var typeData = modificationStateTypes[key];
this._modificationStateTypes.push(new ModificationStateType(typeData, key));
}
}
};
-Configuration.prototype.getModificationStateTypeByName = function(name) {
+Configuration.prototype.getModificationStateTypeByName = function (name) {
var self = this;
for (var i = 0; i < self._modificationStateTypes.length; i++) {
var modificationStateType = self._modificationStateTypes[i];
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 40964f80951dfca19192107f409f9ce127ea462f..64693d0c5dacadc86daf3c28a7e57ebc4268e9c0 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -425,7 +425,11 @@ ServerConnector.idsToString = function (ids) {
var result = "";
if (ids !== undefined) {
ids.sort(function (a, b) {
- return a - b;
+ if (typeof a === "string") {
+ return a.localeCompare(b);
+ } else {
+ return a - b;
+ }
});
for (var i = 0; i < ids.length; i++) {
if (result !== "") {
diff --git a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
index c55f8063bcd6e589b72962ebd8e3cb77c07a7680..1f0cb52ca941f443a321813a5f5cb3c5c4727e6c 100644
--- a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
@@ -19,7 +19,7 @@ function AbstractExportPanel(params) {
AbstractExportPanel.prototype = Object.create(Panel.prototype);
AbstractExportPanel.prototype.constructor = AbstractExportPanel;
-AbstractExportPanel.prototype.init = function() {
+AbstractExportPanel.prototype.init = function () {
};
@@ -33,21 +33,21 @@ function compareSimple(val1, val2) {
}
}
-AbstractExportPanel.prototype._createMiriamTypeDiv = function(annotations) {
+AbstractExportPanel.prototype._createMiriamTypeDiv = function (annotations) {
var self = this;
var typeDiv = Functions.createElement({
- type : "div",
- name : "miriamSelectDiv",
- className : "minerva-export-dual-listbox-container",
+ type: "div",
+ name: "miriamSelectDiv",
+ className: "minerva-export-dual-listbox-container",
});
typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " Annotations:",
+ type: "h4",
+ content: " Annotations:",
}));
var selectElement = Functions.createElement({
- type : "select",
- className : "minerva-multi-select",
+ type: "select",
+ className: "minerva-multi-select",
});
typeDiv.appendChild(selectElement);
@@ -58,6 +58,7 @@ AbstractExportPanel.prototype._createMiriamTypeDiv = function(annotations) {
return compareSimple(-entry1.count, -entry2.count);
}
}
+
annotations.sort(compare);
for (var i = 0; i < annotations.length; i++) {
@@ -68,7 +69,7 @@ AbstractExportPanel.prototype._createMiriamTypeDiv = function(annotations) {
option.value = miriamType.getName();
if (count > 0) {
option.innerHTML = "<div class='minerva-multi-select-special'>" + miriamType.getCommonName() + " (" + count
- + ")</div>";
+ + ")</div>";
} else {
option.innerHTML = "<div >" + miriamType.getCommonName() + "</div>";
}
@@ -79,109 +80,113 @@ AbstractExportPanel.prototype._createMiriamTypeDiv = function(annotations) {
return typeDiv;
};
-AbstractExportPanel.prototype.createDualListbox = function(selectElement) {
+AbstractExportPanel.prototype.createDualListbox = function (selectElement) {
return new DualListbox(selectElement, {
- availableTitle : 'Available',
- selectedTitle : 'Used',
- addButtonText : '>',
- removeButtonText : '<',
- addAllButtonText : '>>',
- removeAllButtonText : '<<'
+ availableTitle: 'Available',
+ selectedTitle: 'Used',
+ addButtonText: '>',
+ removeButtonText: '<',
+ addAllButtonText: '>>',
+ removeAllButtonText: '<<'
});
};
-AbstractExportPanel.prototype._createSelectTypeDiv = function(elementTypes) {
+AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes) {
var typeDiv = Functions.createElement({
- type : "div",
- name : "typeSelectDiv",
+ type: "div",
+ name: "typeSelectDiv",
});
typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " TYPE:",
+ type: "h4",
+ content: " TYPE:",
}));
var choicesContainer = Functions.createElement({
- type : "ul",
- className : "minerva-checkbox-grid"
+ type: "ul",
+ className: "minerva-checkbox-grid"
});
typeDiv.appendChild(choicesContainer);
+ var processedNames = [];
for (var i = 0; i < elementTypes.length; i++) {
var elementType = elementTypes[i];
- var row = Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + elementType + "\" value=\""
- + elementType + "\" />" + elementType + "</label></div>"
- });
- choicesContainer.appendChild(row);
+ var name = elementType.name;
+ if (processedNames[name] === undefined) {
+ processedNames[name] = true;
+ var row = Functions.createElement({
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + name + "\" value=\"" + name + "\" />" + name + "</label></div>"
+ });
+ choicesContainer.appendChild(row);
+ }
}
choicesContainer.appendChild(Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
}));
return typeDiv;
};
-AbstractExportPanel.prototype.getSelectedTypes = function() {
+AbstractExportPanel.prototype.getSelectedTypes = function () {
var self = this;
var div = $("div[name='typeSelectDiv']", $(self.getElement()))[0];
var result = [];
var selectedAll = false;
- $(":checked", $(div)).each(function(index, element) {
+ $(":checked", $(div)).each(function (index, element) {
if (element.value === "ALL") {
selectedAll = true;
}
result.push(element.value);
});
if (selectedAll) {
- return ServerConnector.getConfiguration().then(function(configuration) {
- return configuration.getElementTypes();
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ return configuration.getElementTypeNames();
});
}
return Promise.resolve(result);
};
-AbstractExportPanel.prototype.setMiriamTypesDualListbox = function(dualListbox) {
+AbstractExportPanel.prototype.setMiriamTypesDualListbox = function (dualListbox) {
this._miriamTypesDualListbox = dualListbox;
};
-AbstractExportPanel.prototype.getMiriamTypesDualListbox = function() {
+AbstractExportPanel.prototype.getMiriamTypesDualListbox = function () {
return this._miriamTypesDualListbox;
};
-AbstractExportPanel.prototype._createSelectColumnDiv = function(columnTypes) {
+AbstractExportPanel.prototype._createSelectColumnDiv = function (columnTypes) {
var columnDiv = Functions.createElement({
- type : "div",
- name : "columnSelectDiv",
+ type: "div",
+ name: "columnSelectDiv",
});
columnDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " COLUMN:",
+ type: "h4",
+ content: " COLUMN:",
}));
var choicesContainer = Functions.createElement({
- type : "ul",
- className : "minerva-checkbox-grid"
+ type: "ul",
+ className: "minerva-checkbox-grid"
});
columnDiv.appendChild(choicesContainer);
for (var i = 0; i < columnTypes.length; i++) {
var columnType = columnTypes[i];
var row = Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"column_" + columnType.columnName
- + "\" value=\"" + columnType.columnName + "\" />" + columnType.name + "</label></div>"
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"column_" + columnType.columnName
+ + "\" value=\"" + columnType.columnName + "\" />" + columnType.name + "</label></div>"
});
choicesContainer.appendChild(row);
}
choicesContainer.appendChild(Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
}));
return columnDiv;
};
-AbstractExportPanel.prototype.getSelectedMiriamTypes = function() {
+AbstractExportPanel.prototype.getSelectedMiriamTypes = function () {
var self = this;
- return ServerConnector.getConfiguration().then(function(configuration) {
+ return ServerConnector.getConfiguration().then(function (configuration) {
var selected = self.getMiriamTypesDualListbox().selected;
var result = [];
for (var i = 0; i < selected.length; i++) {
@@ -192,13 +197,13 @@ AbstractExportPanel.prototype.getSelectedMiriamTypes = function() {
});
};
-AbstractExportPanel.prototype.getSelectedColumns = function() {
+AbstractExportPanel.prototype.getSelectedColumns = function () {
var self = this;
var div = $("div[name='columnSelectDiv']", $(self.getElement()))[0];
var selectedColumnMap = [];
var selectedAll = false;
- $(":checked", $(div)).each(function(index, element) {
+ $(":checked", $(div)).each(function (index, element) {
if (element.value === "ALL") {
selectedAll = true;
}
@@ -221,10 +226,10 @@ AbstractExportPanel.prototype.getSelectedColumns = function() {
return Promise.resolve(result);
};
-AbstractExportPanel.prototype._getCompartmentNames = function() {
+AbstractExportPanel.prototype._getCompartmentNames = function () {
var self = this;
var compartments = [];
- return self._getAllCompartments().then(function(result) {
+ return self._getAllCompartments().then(function (result) {
var addedNames = [];
for (var i = 0; i < result.length; i++) {
@@ -238,16 +243,16 @@ AbstractExportPanel.prototype._getCompartmentNames = function() {
});
};
-AbstractExportPanel.prototype.getModels = function() {
+AbstractExportPanel.prototype.getModels = function () {
var self = this;
- var models = [ self.getProject().getModel() ];
+ var models = [self.getProject().getModel()];
for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
models.push(self.getProject().getModel().getSubmodels()[i]);
}
return models;
};
-AbstractExportPanel.prototype._getAllCompartments = function() {
+AbstractExportPanel.prototype._getAllCompartments = function () {
var self = this;
var compartments = [];
@@ -258,7 +263,7 @@ AbstractExportPanel.prototype._getAllCompartments = function() {
promises.push(models[i].getCompartments());
}
- return Promise.all(promises).then(function(result) {
+ return Promise.all(promises).then(function (result) {
for (var i = 0; i < result.length; i++) {
var modelCompartments = result[i];
for (var j = 0; j < modelCompartments.length; j++) {
@@ -269,28 +274,28 @@ AbstractExportPanel.prototype._getAllCompartments = function() {
});
};
-AbstractExportPanel.prototype._createDownloadButton = function() {
+AbstractExportPanel.prototype._createDownloadButton = function () {
var self = this;
var downloadDiv = Functions.createElement({
- type : "div",
- name : "downloadDiv",
- style : "clear:both; padding: 10px;",
+ type: "div",
+ name: "downloadDiv",
+ style: "clear:both; padding: 10px;",
});
var button = Functions.createElement({
- type : "button",
- name : "downloadButton",
- content : " Download",
- onclick : function() {
+ type: "button",
+ name: "downloadButton",
+ content: " Download",
+ onclick: function () {
GuiConnector.showProcessing();
- return self.createResponseString().then(function(result) {
- var blob = new Blob([ result ], {
- type : "text/plain;charset=utf-8"
+ return self.createResponseString().then(function (result) {
+ var blob = new Blob([result], {
+ type: "text/plain;charset=utf-8"
});
var FileSaver = require("file-saver");
return FileSaver.saveAs(blob, self.getSaveFilename());
- }).then(function() {
+ }).then(function () {
GuiConnector.hideProcessing();
- }, function(error) {
+ }, function (error) {
GuiConnector.hideProcessing();
GuiConnector.alert(error);
});
@@ -301,28 +306,28 @@ AbstractExportPanel.prototype._createDownloadButton = function() {
return downloadDiv;
};
-AbstractExportPanel.prototype.getSaveFilename = function() {
+AbstractExportPanel.prototype.getSaveFilename = function () {
var self = this;
return self.getProject().getProjectId() + "-" + self.getPanelName() + ".txt";
};
-AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function() {
+AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function () {
var self = this;
var typeDiv = Functions.createElement({
- type : "div",
- name : "includedCompartmentSelectDiv",
- className : "minerva-export-dual-listbox-container",
+ type: "div",
+ name: "includedCompartmentSelectDiv",
+ className: "minerva-export-dual-listbox-container",
});
typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " Included compartment/pathways:",
+ type: "h4",
+ content: " Included compartment/pathways:",
}));
- return self._getCompartmentNames().then(function(compartmentNames) {
+ return self._getCompartmentNames().then(function (compartmentNames) {
var selectElement = Functions.createElement({
- type : "select",
- className : "minerva-multi-select",
+ type: "select",
+ className: "minerva-multi-select",
});
typeDiv.appendChild(selectElement);
@@ -339,23 +344,23 @@ AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function() {
});
};
-AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function() {
+AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function () {
var self = this;
var typeDiv = Functions.createElement({
- type : "div",
- name : "excludedCompartmentSelectDiv",
- className : "minerva-export-dual-listbox-container",
+ type: "div",
+ name: "excludedCompartmentSelectDiv",
+ className: "minerva-export-dual-listbox-container",
});
typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " Excluded compartment/pathways:",
+ type: "h4",
+ content: " Excluded compartment/pathways:",
}));
- return self._getCompartmentNames().then(function(compartmentNames) {
+ return self._getCompartmentNames().then(function (compartmentNames) {
var selectElement = Functions.createElement({
- type : "select",
- className : "minerva-multi-select",
+ type: "select",
+ className: "minerva-multi-select",
});
typeDiv.appendChild(selectElement);
@@ -372,14 +377,14 @@ AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function() {
});
};
-AbstractExportPanel.prototype.setIncludedCompartmentsDualListbox = function(dualListbox) {
+AbstractExportPanel.prototype.setIncludedCompartmentsDualListbox = function (dualListbox) {
this._includedCompartmentsDualListbox = dualListbox;
};
-AbstractExportPanel.prototype.getIncludedCompartmentsDualListbox = function() {
+AbstractExportPanel.prototype.getIncludedCompartmentsDualListbox = function () {
return this._includedCompartmentsDualListbox;
};
-AbstractExportPanel.prototype.getSelectedIncludedCompartments = function() {
+AbstractExportPanel.prototype.getSelectedIncludedCompartments = function () {
var self = this;
var list = self.getIncludedCompartmentsDualListbox().selected;
var names = [];
@@ -388,7 +393,7 @@ AbstractExportPanel.prototype.getSelectedIncludedCompartments = function() {
var element = list[i];
names[element.dataset.id] = true;
}
- return self._getAllCompartments().then(function(compartments) {
+ return self._getAllCompartments().then(function (compartments) {
for (var i = 0; i < compartments.length; i++) {
var compartment = compartments[i];
if (names[compartment.getName()]) {
@@ -399,14 +404,14 @@ AbstractExportPanel.prototype.getSelectedIncludedCompartments = function() {
});
};
-AbstractExportPanel.prototype.setExcludedCompartmentsDualListbox = function(dualListbox) {
+AbstractExportPanel.prototype.setExcludedCompartmentsDualListbox = function (dualListbox) {
this._excludedCompartmentsDualListbox = dualListbox;
};
-AbstractExportPanel.prototype.getExcludedCompartmentsDualListbox = function() {
+AbstractExportPanel.prototype.getExcludedCompartmentsDualListbox = function () {
return this._excludedCompartmentsDualListbox;
};
-AbstractExportPanel.prototype.getSelectedExcludedCompartments = function() {
+AbstractExportPanel.prototype.getSelectedExcludedCompartments = function () {
var self = this;
var list = self.getExcludedCompartmentsDualListbox().selected;
var names = [];
@@ -415,7 +420,7 @@ AbstractExportPanel.prototype.getSelectedExcludedCompartments = function() {
var element = list[i];
names[element.dataset.id] = true;
}
- return self._getAllCompartments().then(function(compartments) {
+ return self._getAllCompartments().then(function (compartments) {
for (var i = 0; i < compartments.length; i++) {
var compartment = compartments[i];
if (names[compartment.getName()]) {
@@ -426,7 +431,7 @@ AbstractExportPanel.prototype.getSelectedExcludedCompartments = function() {
});
};
-AbstractExportPanel.prototype.createResponseHeader = function(columns, miriamTypes) {
+AbstractExportPanel.prototype.createResponseHeader = function (columns, miriamTypes) {
var stringBuilder = [];
var i;
for (i = 0; i < columns.length; i++) {
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index deed136a3b0d68743e29305d3b3038694cf32e99..3e3ece2499c8e66f91f8e960b5f6c66503d1e808 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -298,7 +298,7 @@ function createResult(customMap) {
options: {
icon: identifiedElements[i].getIcon(),
color: identifiedElements[i].getColor(),
- opacity: identifiedElements[i].getOpacity(),
+ opacity: identifiedElements[i].getOpacity()
}
};
result.push(row);
@@ -336,8 +336,8 @@ function createResult(customMap) {
var promises = [];
for (i = 0; i < models.length; i++) {
promises.push(models[i].getAliases({
- type: customMap.getConfiguration().getElementTypes(),
- complete: true,
+ type: customMap.getConfiguration().getElementTypeNames(),
+ complete: true
}));
}
return Promise.all(promises).then(function (aliasesByModel) {
@@ -427,7 +427,7 @@ function createResult(customMap) {
throw new Error("Unknown modelId: " + params.modelId);
}
return submap.setZoom(params.zoom);
- },
+ }
};
}
diff --git a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
index 209fd20b97e369a40fdc584c867db855aa3be2b4..5dd005df320989e2dc61ce82fd67950673784e34 100644
--- a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
+++ b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
@@ -43,7 +43,7 @@ describe('ElementExportPanel', function() {
return ServerConnector.getConfiguration().then(function(result) {
configuration = result;
- elementTypes = configuration.getElementTypes();
+ elementTypes = configuration.getElementTypeNames();
return ServerConnector.getProject();
}).then(function(result) {
project = result;
diff --git a/frontend-js/src/test/js/gui/export/NetworkExportPanel-test.js b/frontend-js/src/test/js/gui/export/NetworkExportPanel-test.js
index 1badab9af1c93d8f392d50ae969c9e3d34b91b29..814080ba54ae225f5ea084b2b717fef66daa599a 100644
--- a/frontend-js/src/test/js/gui/export/NetworkExportPanel-test.js
+++ b/frontend-js/src/test/js/gui/export/NetworkExportPanel-test.js
@@ -2,6 +2,8 @@
/* exported logger */
+require("../../mocha-config");
+
var NetworkExportPanel = require('../../../../main/js/gui/export/NetworkExportPanel');
var logger = require('../../logger');
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index ace46e3e106afa218f01fb5261f6b27bf1ca8fc8..383ef3a60bc41283be90bdae720702046dd329fd 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -1,5 +1,7 @@
"use strict";
+require("./mocha-config");
+
var Helper = require('./helper');
require("./mocha-config.js");
diff --git a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
index 3021fe2f6d3bd325e8474c00089229085fb61a43..1fd5b097b6c6e6791eb1f3b22f1d66482b974805 100644
--- a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"modelFormats":[{"handler":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser","extension":"xml","name":"CellDesigner SBML"},{"handler":"lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter","extension":"sbgn","name":"SBGN-ML"}],"elementTypes":["Drug","Degraded","Phenotype","Gene","RNA","Unknown","Compartment","Antisense RNA","Ion","Simple 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Reaction","uris":["urn:miriam:kegg.reaction"],"homepage":"http://www.genome.jp/kegg/reaction/","registryIdentifier":"MIR:00000014"},"KEGG_ORTHOLOGY":{"commonName":"KEGG Orthology","uris":["urn:miriam:kegg.orthology"],"homepage":"http://www.genome.jp/kegg/ko.html","registryIdentifier":"MIR:00000116"},"PUBCHEM":{"commonName":"PubChem-compound","uris":["urn:miriam:pubchem.compound"],"homepage":"http://pubchem.ncbi.nlm.nih.gov/","registryIdentifier":"MIR:00000034"},"MESH_2012":{"commonName":"MeSH 2012","uris":["urn:miriam:mesh.2012","urn:miriam:mesh"],"homepage":"http://www.nlm.nih.gov/mesh/","registryIdentifier":"MIR:00000270"},"MGD":{"commonName":"Mouse Genome Database","uris":["urn:miriam:mgd"],"homepage":"http://www.informatics.jax.org/","registryIdentifier":"MIR:00000037"},"ENTREZ":{"commonName":"Entrez 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image"},{"handler":"lcsb.mapviewer.converter.graphics.PdfImageGenerator","extension":"pdf","name":"PDF"},{"handler":"lcsb.mapviewer.converter.graphics.SvgImageGenerator","extension":"svg","name":"SVG image"}],"options":[{"idObject":9,"type":"EMAIL_ADDRESS","value":"your.account@domain.com"},{"idObject":10,"type":"EMAIL_LOGIN","value":"your@login"},{"idObject":11,"type":"EMAIL_PASSWORD","value":"email.secret.password"},{"idObject":13,"type":"EMAIL_IMAP_SERVER","value":"your.imap.domain.com"},{"idObject":12,"type":"EMAIL_SMTP_SERVER","value":"your.smtp.domain.com"},{"idObject":14,"type":"EMAIL_SMTP_PORT","value":"25"},{"idObject":6,"type":"DEFAULT_MAP","value":"sample"},{"idObject":4,"type":"LOGO_IMG","value":"udl.png"},{"idObject":3,"type":"LOGO_LINK","value":"http://wwwen.uni.lu/"},{"idObject":7,"type":"SEARCH_DISTANCE","value":"10"},{"idObject":1,"type":"REQUEST_ACCOUNT_EMAIL","value":"your.email@domain.com"},{"idObject":8,"type":"SEARCH_RESULT_NUMBER","value":"100"},{"idObject":2,"type":"GOOGLE_ANALYTICS_IDENTIFIER","value":""},{"idObject":5,"type":"LOGO_TEXT","value":"University of Luxembourg"},{"idObject":56,"type":"X_FRAME_DOMAIN","value":"http://localhost:8080/"},{"idObject":131,"type":"BIG_FILE_STORAGE_DIR","value":"minerva-big/"},{"idObject":138,"type":"LENGEND_FILE_1","value":"resources/images/legend_a.png"},{"idObject":139,"type":"LENGEND_FILE_2","value":"resources/images/legend_b.png"},{"idObject":140,"type":"LENGEND_FILE_3","value":"resources/images/legend_c.png"},{"idObject":141,"type":"LENGEND_FILE_4","value":"resources/images/legend_d.png"},{"idObject":142,"type":"USER_MANUAL_FILE","value":"resources/other/user_guide.pdf"},{"idObject":205,"type":"MIN_COLOR_VAL","value":"FF0000"},{"idObject":206,"type":"MAX_COLOR_VAL","value":"fbff00"},{"idObject":218,"type":"SIMPLE_COLOR_VAL","value":"00FF00"}],"privilegeTypes":{"VIEW_PROJECT":{"commonName":"View project","valueType":"boolean","objectType":"Project"},"LAYOUT_MANAGEMENT":{"commonName":"Manage layouts","valueType":"boolean","objectType":"Project"},"PROJECT_MANAGEMENT":{"commonName":"Map 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transition","Truncation","Reduced trigger","Boolean logic gate","Unknown reduced physical stimulation","Generic Reaction","Reduced modulation","Unknown negative influence","Heterodimer association","Dissociation","Known transition omitted","Transport"]}
\ No newline at end of file
+{"modelFormats":[{"handler":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser","extension":"xml","name":"CellDesigner SBML"},{"handler":"lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter","extension":"sbgn","name":"SBGN-ML"}],"elementTypes":[{"name":"Ion","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Simple molecule","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Degraded","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Complex","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Antisense RNA","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Phenotype","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Gene","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"RNA","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Drug","className":"lcsb.mapviewer.model.map.species.Element"},{"name":"Unknown","className":"lcsb.mapviewer.model.map.species.Element"}],"modificationStateTypes":{"PHOSPHORYLATED":{"commonName":"phosphorylated","abbreviation":"P"},"METHYLATED":{"commonName":"methylated","abbreviation":"Me"},"PALMYTOYLATED":{"commonName":"palmytoylated","abbreviation":"Pa"},"ACETYLATED":{"commonName":"acetylated","abbreviation":"Ac"},"SULFATED":{"commonName":"sulfated","abbreviation":"S"},"GLYCOSYLATED":{"commonName":"glycosylated","abbreviation":"G"},"PRENYLATED":{"commonName":"prenylated","abbreviation":"Pr"},"UBIQUITINATED":{"commonName":"ubiquitinated","abbreviation":"Ub"},"PROTONATED":{"commonName":"protonated","abbreviation":"H"},"HYDROXYLATED":{"commonName":"hydroxylated","abbreviation":"OH"},"MYRISTOYLATED":{"commonName":"myristoylated","abbreviation":"My"},"UNKNOWN":{"commonName":"unknown","abbreviation":"?"},"EMPTY":{"commonName":"empty","abbreviation":""},"DONT_CARE":{"commonName":"don't 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Groups","uris":["urn:miriam:cogs"],"homepage":"https://www.ncbi.nlm.nih.gov/COG/","registryIdentifier":"MIR:00000296"},"WIKIPATHWAYS":{"commonName":"WikiPathways","uris":["urn:miriam:wikipathways"],"homepage":"http://www.wikipathways.org/","registryIdentifier":"MIR:00000076"},"HMDB":{"commonName":"HMDB","uris":["urn:miriam:hmdb"],"homepage":"http://www.hmdb.ca/","registryIdentifier":"MIR:00000051"},"CHEMSPIDER":{"commonName":"ChemSpider","uris":["urn:miriam:chemspider"],"homepage":"http://www.chemspider.com//","registryIdentifier":"MIR:00000138"},"ENSEMBL":{"commonName":"Ensembl","uris":["urn:miriam:ensembl"],"homepage":"www.ensembl.org","registryIdentifier":"MIR:00000003"},"GO":{"commonName":"Gene Ontology","uris":["urn:miriam:obo.go","urn:miriam:go"],"homepage":"http://amigo.geneontology.org/amigo","registryIdentifier":"MIR:00000022"},"KEGG_REACTION":{"commonName":"Kegg Reaction","uris":["urn:miriam:kegg.reaction"],"homepage":"http://www.genome.jp/kegg/reaction/","registryIdentifier":"MIR:00000014"},"KEGG_ORTHOLOGY":{"commonName":"KEGG Orthology","uris":["urn:miriam:kegg.orthology"],"homepage":"http://www.genome.jp/kegg/ko.html","registryIdentifier":"MIR:00000116"},"PUBCHEM":{"commonName":"PubChem-compound","uris":["urn:miriam:pubchem.compound"],"homepage":"http://pubchem.ncbi.nlm.nih.gov/","registryIdentifier":"MIR:00000034"},"MESH_2012":{"commonName":"MeSH 2012","uris":["urn:miriam:mesh.2012","urn:miriam:mesh"],"homepage":"http://www.nlm.nih.gov/mesh/","registryIdentifier":"MIR:00000270"},"MGD":{"commonName":"Mouse Genome Database","uris":["urn:miriam:mgd"],"homepage":"http://www.informatics.jax.org/","registryIdentifier":"MIR:00000037"},"ENTREZ":{"commonName":"Entrez Gene","uris":["urn:miriam:ncbigene","urn:miriam:entrez.gene"],"homepage":"http://www.ncbi.nlm.nih.gov/gene","registryIdentifier":"MIR:00000069"},"PUBCHEM_SUBSTANCE":{"commonName":"PubChem-substance","uris":["urn:miriam:pubchem.substance"],"homepage":"http://pubchem.ncbi.nlm.nih.gov/","registryIdentifier":"MIR:00000033"},"CCDS":{"commonName":"Consensus CDS","uris":["urn:miriam:ccds"],"homepage":"http://www.ncbi.nlm.nih.gov/CCDS/","registryIdentifier":"MIR:00000375"},"KEGG_GENES":{"commonName":"Kegg Genes","uris":["urn:miriam:kegg.genes","urn:miriam:kegg.genes:hsa"],"homepage":"http://www.genome.jp/kegg/genes.html","registryIdentifier":"MIR:00000070"},"TOXICOGENOMIC_CHEMICAL":{"commonName":"Toxicogenomic Chemical","uris":["urn:miriam:ctd.chemical"],"homepage":"http://ctdbase.org/","registryIdentifier":"MIR:00000098"},"SGD":{"commonName":"Saccharomyces Genome Database","uris":["urn:miriam:sgd"],"homepage":"http://www.yeastgenome.org/","registryIdentifier":"MIR:00000023"},"KEGG_COMPOUND":{"commonName":"Kegg Compound","uris":["urn:miriam:kegg.compound"],"homepage":"http://www.genome.jp/kegg/ligand.html","registryIdentifier":"MIR:00000013"},"INTERPRO":{"commonName":"InterPro","uris":["urn:miriam:interpro"],"homepage":"http://www.ebi.ac.uk/interpro/","registryIdentifier":"MIR:00000011"},"UNKNOWN":{"commonName":"Unknown","uris":[],"homepage":null,"registryIdentifier":null},"DRUGBANK":{"commonName":"DrugBank","uris":["urn:miriam:drugbank"],"homepage":"http://www.drugbank.ca/","registryIdentifier":"MIR:00000102"},"PUBMED":{"commonName":"PubMed","uris":["urn:miriam:pubmed"],"homepage":"http://www.ncbi.nlm.nih.gov/PubMed/","registryIdentifier":"MIR:00000015"}},"imageFormats":[{"handler":"lcsb.mapviewer.converter.graphics.PngImageGenerator","extension":"png","name":"PNG image"},{"handler":"lcsb.mapviewer.converter.graphics.PdfImageGenerator","extension":"pdf","name":"PDF"},{"handler":"lcsb.mapviewer.converter.graphics.SvgImageGenerator","extension":"svg","name":"SVG image"}],"options":[{"idObject":9,"type":"EMAIL_ADDRESS","value":"your.account@domain.com"},{"idObject":10,"type":"EMAIL_LOGIN","value":"your@login"},{"idObject":11,"type":"EMAIL_PASSWORD","value":"email.secret.password"},{"idObject":13,"type":"EMAIL_IMAP_SERVER","value":"your.imap.domain.com"},{"idObject":12,"type":"EMAIL_SMTP_SERVER","value":"your.smtp.domain.com"},{"idObject":14,"type":"EMAIL_SMTP_PORT","value":"25"},{"idObject":6,"type":"DEFAULT_MAP","value":"sample"},{"idObject":4,"type":"LOGO_IMG","value":"udl.png"},{"idObject":3,"type":"LOGO_LINK","value":"http://wwwen.uni.lu/"},{"idObject":7,"type":"SEARCH_DISTANCE","value":"10"},{"idObject":1,"type":"REQUEST_ACCOUNT_EMAIL","value":"your.email@domain.com"},{"idObject":8,"type":"SEARCH_RESULT_NUMBER","value":"100"},{"idObject":2,"type":"GOOGLE_ANALYTICS_IDENTIFIER","value":""},{"idObject":5,"type":"LOGO_TEXT","value":"University of Luxembourg"},{"idObject":56,"type":"X_FRAME_DOMAIN","value":"http://localhost:8080/"},{"idObject":131,"type":"BIG_FILE_STORAGE_DIR","value":"minerva-big/"},{"idObject":138,"type":"LEGEND_FILE_1","value":"resources/images/legend_a.png"},{"idObject":139,"type":"LEGEND_FILE_2","value":"resources/images/legend_b.png"},{"idObject":140,"type":"LEGEND_FILE_3","value":"resources/images/legend_c.png"},{"idObject":141,"type":"LEGEND_FILE_4","value":"resources/images/legend_d.png"},{"idObject":142,"type":"USER_MANUAL_FILE","value":"resources/other/user_guide.pdf"},{"idObject":205,"type":"MIN_COLOR_VAL","value":"FF0000"},{"idObject":206,"type":"MAX_COLOR_VAL","value":"fbff00"},{"idObject":218,"type":"SIMPLE_COLOR_VAL","value":"00FF00"}],"privilegeTypes":{"VIEW_PROJECT":{"commonName":"View project","valueType":"boolean","objectType":"Project"},"LAYOUT_MANAGEMENT":{"commonName":"Manage layouts","valueType":"boolean","objectType":"Project"},"PROJECT_MANAGEMENT":{"commonName":"Map management","valueType":"boolean","objectType":null},"CUSTOM_LAYOUTS":{"commonName":"Custom layouts","valueType":"int","objectType":null},"ADD_MAP":{"commonName":"Add project","valueType":"boolean","objectType":null},"LAYOUT_VIEW":{"commonName":"View layout","valueType":"boolean","objectType":"Layout"},"MANAGE_GENOMES":{"commonName":"Manage genomes","valueType":"boolean","objectType":null},"EDIT_COMMENTS_PROJECT":{"commonName":"Manage comments","valueType":"boolean","objectType":"Project"},"CONFIGURATION_MANAGE":{"commonName":"Manage configuration","valueType":"boolean","objectType":null},"USER_MANAGEMENT":{"commonName":"User management","valueType":"boolean","objectType":null}},"overlayTypes":[{"name":"GENERIC"},{"name":"GENETIC_VARIANT"}],"buildDate":"29/08/2017 18:52","reactionTypes":[{"name":"Unknown reduced modulation","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced physical stimulation","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"State transition","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Translation","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Transport","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Heterodimer association","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Dissociation","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Positive influence","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Transcription","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced trigger","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced physical stimulation","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Negative influence","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Boolean logic gate","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced trigger","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Truncation","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown transition","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown positive influence","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Known transition omitted","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Generic Reaction","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown negative influence","className":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced modulation","className":"lcsb.mapviewer.model.map.reaction.Reaction"}],"version":"11.0.0"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,removed,pinned,author,email&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=author,elementId,email,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,removed,pinned,author,email&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=author,elementId,email,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,icon,removed,pinned&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,icon,removed,pinned&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,icon,removed&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,removed,type&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=id,elementId,modelId,type,icon,removed&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,removed,type&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Antisense RNA,Compartment,Complex,Degraded,Drug,Gene,Ion,Phenotype,Protein,RNA,Simple molecule,Unknown&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Antisense RNA,Compartment,Complex,Degraded,Drug,Gene,Ion,Phenotype,Protein,RNA,Simple molecule,Unknown&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Antisense RNA,Compartment,Complex,Degraded,Drug,Gene,Ion,Phenotype,Protein,RNA,Simple molecule,Unknown&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Antisense RNA,Compartment,Complex,Degraded,Drug,Gene,Ion,Phenotype,Protein,RNA,Simple molecule,Unknown&token=MOCK_TOKEN_ID&
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index 8ff0f95344526a7e9e12cd455af360f510d71a1d..699a165978a232fed7df2c3f81ddfeb1d5c3340b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -96,22 +96,22 @@ public enum ConfigurationElementType {
/**
* File where legend 1/4 is stored.
*/
- LENGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png", ConfigurationElementEditType.URL, false),
+ LEGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png", ConfigurationElementEditType.URL, false),
/**
* File where legend 2/4 is stored.
*/
- LENGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png", ConfigurationElementEditType.URL, false),
+ LEGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png", ConfigurationElementEditType.URL, false),
/**
* File where legend 3/4 is stored.
*/
- LENGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png", ConfigurationElementEditType.URL, false),
+ LEGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png", ConfigurationElementEditType.URL, false),
/**
* File where legend 4/4 is stored.
*/
- LENGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png", ConfigurationElementEditType.URL, false),
+ LEGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png", ConfigurationElementEditType.URL, false),
/**
* File where legend 4/4 is stored.
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
index 3346fc3cb1d41f5bdc40089a34072f8a47bf144b..1450e9a8bef1be8410e2425be86c9951ac9c9017 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
@@ -3,6 +3,8 @@ package lcsb.mapviewer.api.configuration;
import java.util.HashMap;
import java.util.Map;
+import javax.servlet.ServletContext;
+
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.CookieValue;
@@ -13,11 +15,21 @@ import org.springframework.web.bind.annotation.RestController;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
@RestController
public class ConfigurationController extends BaseController {
@Autowired
- private ConfigurationRestImpl configurationController;
+ private ConfigurationRestImpl configurationController;
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ /**
+ * Context used to determine deployment path.
+ */
+ @Autowired
+ private ServletContext context;
@RequestMapping(value = "/configuration/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getOverlayTypes(@CookieValue(value = Configuration.AUTH_TOKEN) String token) throws SecurityException {
@@ -31,6 +43,8 @@ public class ConfigurationController extends BaseController {
result.put("miriamTypes", configurationController.getMiriamTypes(token));
result.put("modificationStateTypes", configurationController.getModificationStateTypes(token));
result.put("privilegeTypes", configurationController.getPrivilegeTypes(token));
+ result.put("version", configurationService.getSystemSvnVersion(context.getRealPath("/")));
+ result.put("buildDate", configurationService.getSystemBuild(context.getRealPath("/")));
return result;
}
@@ -51,4 +65,21 @@ public class ConfigurationController extends BaseController {
this.configurationController = configurationController;
}
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 5b74c890ebabd216e77e12815afe00aa7d30f994..1c7329d6a647cc6ffeafcd9ac033cf84898b0425 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -134,14 +134,14 @@ public class ConfigurationRestImpl {
return result;
}
- public Set<String> getElementTypes(String token) throws SecurityException {
+ public Set<Map<String, String>> getElementTypes(String token) throws SecurityException {
userService.getToken(token);
return getClassStringTypesList(Element.class);
}
- private Set<String> getClassStringTypesList(Class<?> elementClass) {
- Set<String> result = new HashSet<>();
+ private Set<Map<String, String>> getClassStringTypesList(Class<?> elementClass) {
+ Set<Map<String, String>> result = new HashSet<>();
ElementUtils elementUtils = new ElementUtils();
ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
Queue<ClassTreeNode> queue = new LinkedList<>();
@@ -153,12 +153,18 @@ public class ConfigurationRestImpl {
}
if (elementClass.isAssignableFrom(clazz.getClazz())) {
if (!Modifier.isAbstract(clazz.getClazz().getModifiers())) {
+ Map<String, String> row = new HashMap<>();
try {
+ row.put("className", elementClass.getName());
+ String name = null;
if (elementClass.isAssignableFrom(Reaction.class)) {
- result.add(((BioEntity) (clazz.getClazz().getDeclaredConstructor().newInstance())).getStringType());
+ row.put("className", elementClass.getName());
+ name = ((BioEntity) (clazz.getClazz().getDeclaredConstructor().newInstance())).getStringType();
} else {
- result.add(((BioEntity) (clazz.getClazz().getDeclaredConstructor(String.class).newInstance("id"))).getStringType());
+ name = ((BioEntity) (clazz.getClazz().getDeclaredConstructor(String.class).newInstance("id"))).getStringType();
}
+ row.put("name", name);
+ result.add(row);
} catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException
| java.lang.SecurityException e) {
throw new RuntimeException(e);
@@ -169,7 +175,7 @@ public class ConfigurationRestImpl {
return result;
}
- public Set<String> getReactionTypes(String token) throws SecurityException {
+ public Set<Map<String, String>> getReactionTypes(String token) throws SecurityException {
userService.getToken(token);
return getClassStringTypesList(Reaction.class);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index 621a0dd6d64839e716e89d2742381313bec10858..5b8e4672b56384b49e27ea69a1f509b94cd90894 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -94,6 +94,17 @@ public class UserController extends BaseController {
return userRest.updatePrivileges(token, login, data);
}
+ @RequestMapping(value = "/users/{login}:updatePreferences", method = { RequestMethod.PATCH }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> updatePreferences(//
+ @RequestBody String body, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "login") String login //
+ ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "preferences");
+ return userRest.updatePreferences(token, login, data);
+ }
+
@RequestMapping(value = "/users/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public List<Map<String, Object>> getUsers(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
index 52b5c6aa884540de6efa5ed1602bf858750a62a2..fe90900409938f0ecef9997959c126b825a84572 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
@@ -76,9 +76,13 @@ public class ConfigurationRestImplTest extends RestTestFunctions {
@Test
public void testGetElementTypes() throws Exception {
try {
- Set<String> list = configurationRestImpl.getElementTypes(token.getId());
+ Set<Map<String, String>> list = configurationRestImpl.getElementTypes(token.getId());
GenericProtein protein = new GenericProtein("id");
- assertTrue(list.contains(protein.getStringType()));
+ boolean contains = false;
+ for (Map<String, String> object : list) {
+ contains |= (object.get("name").equals(protein.getStringType()));
+ }
+ assertTrue(contains);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -88,9 +92,13 @@ public class ConfigurationRestImplTest extends RestTestFunctions {
@Test
public void testGetReactionTypes() throws Exception {
try {
- Set<String> list = configurationRestImpl.getReactionTypes(token.getId());
- StateTransitionReaction protein = new StateTransitionReaction();
- assertTrue(list.contains(protein.getStringType()));
+ Set<Map<String, String>> list = configurationRestImpl.getReactionTypes(token.getId());
+ StateTransitionReaction reaction = new StateTransitionReaction();
+ boolean contains = false;
+ for (Map<String, String> object : list) {
+ contains |= (object.get("name").equals(reaction.getStringType()));
+ }
+ assertTrue(contains);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -100,7 +108,7 @@ public class ConfigurationRestImplTest extends RestTestFunctions {
@Test
public void testGetMiriamTypes() throws Exception {
try {
- Map<?,?> list = configurationRestImpl.getMiriamTypes(token.getId());
+ Map<?, ?> list = configurationRestImpl.getMiriamTypes(token.getId());
assertNotNull(list.get(MiriamType.PUBMED.name()));
} catch (Exception e) {
e.printStackTrace();
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java b/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
index 7fcd49d3a7afc1cf58b49cb8666a2d3d4f06e846..b93fdd83be4beaa8cbf60a0da5a956f6af3e40ac 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
@@ -422,39 +422,39 @@ public class ConfigurationBean extends AbstractManagedBean implements Serializab
}
/**
- * Returns {@link ConfigurationElementType#LENGEND_FILE_1 legend file 1}.
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}.
*
- * @return {@link ConfigurationElementType#LENGEND_FILE_1 legend file 1}
+ * @return {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}
*/
public String getLegendFile1() {
- return valueMap.get(ConfigurationElementType.LENGEND_FILE_1);
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_1);
}
/**
- * Returns {@link ConfigurationElementType#LENGEND_FILE_2 legend file 2}.
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}.
*
- * @return {@link ConfigurationElementType#LENGEND_FILE_2 legend file 2}
+ * @return {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}
*/
public String getLegendFile2() {
- return valueMap.get(ConfigurationElementType.LENGEND_FILE_2);
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_2);
}
/**
- * Returns {@link ConfigurationElementType#LENGEND_FILE_3 legend file 3}.
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}.
*
- * @return {@link ConfigurationElementType#LENGEND_FILE_3 legend file 3}
+ * @return {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}
*/
public String getLegendFile3() {
- return valueMap.get(ConfigurationElementType.LENGEND_FILE_3);
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_3);
}
/**
- * Returns {@link ConfigurationElementType#LENGEND_FILE_4 legend file 4}.
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}.
*
- * @return {@link ConfigurationElementType#LENGEND_FILE_4 legend file 4}
+ * @return {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}
*/
public String getLegendFile4() {
- return valueMap.get(ConfigurationElementType.LENGEND_FILE_4);
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_4);
}
/**