Merge branch 'develop'

ChangeLog.md

@@ -1,4 +1,17 @@
 
+
+## 2.4.1
+
+Features
+
+- Organism and Group tab should searchable.  [2081](https://github.com/GMOD/Apollo/pull/2081) 
+
+Bug
+
+- Bump JBrowse version to 1.16.6 to fix drag error on Chrome mac. <https://github.com/GMOD/jbrowse/issues/1397>
+
+
+
 ## 2.4.0
 
  Features

README.md

@@ -29,7 +29,7 @@ Launchable public Amazon Web Services (AWS) EC2 images may be [launched from Com
 Launch settings should be 2 vCPU, 8 GB recommended, 80 GB storage depending on the size of your data, and ports 22 and 8080 open at a minimum.
 The server will be available at <http://aws.public.ip:8080/apollo/>.   Binaries with be in the `apollo/bin` directory though it should be in the path.
 
-Apollo may be launched from [Docker](docs/Setup.md#configure-for-docker) as well. 
+Apollo may be launched from [Docker](docs/Docker.md) as well. 
 
 The [quick-start guide for developers](docs/Apollo2Build.md) shows how to easily get started with Apollo. 
 

application.properties

@@ -3,4 +3,4 @@
 app.grails.version=2.5.5
 app.name=apollo
 app.servlet.version=3.0
-app.version=2.4.0
+app.version=2.4.1

docker-files/createenv.sh

@@ -47,3 +47,6 @@ echo "export APOLLO_ADMIN_PASSWORD=$APOLLO_ADMIN_PASSWORD" >> $SET_ENV_FILE
 echo "export APOLLO_ADMIN_FIRST_NAME=$APOLLO_ADMIN_FIRST_NAME" >> $SET_ENV_FILE
 echo "export APOLLO_ADMIN_LAST_NAME=$APOLLO_ADMIN_LAST_NAME" >> $SET_ENV_FILE
 
+# If we want to change authentication methods
+echo "export WEBAPOLLO_REMOTE_USER_AUTH=$WEBAPOLLO_REMOTE_USER_AUTH" >> $SET_ENV_FILE
+echo "export WEBAPOLLO_USER_PASSWORD_AUTH=$WEBAPOLLO_USER_PASSWORD_AUTH" >> $SET_ENV_FILE

docker-files/docker-apollo-config.groovy

@@ -106,6 +106,18 @@ apollo {
         firstName = System.getenv("APOLLO_ADMIN_FIRST_NAME") ?: "Ad"
         lastName = System.getenv("APOLLO_ADMIN_LAST_NAME") ?: "min"
     }
+    authentications = [
+        [
+            "name":"Remote User Authenticator",
+            "className":"remoteUserAuthenticatorService",
+            "active": System.getenv("WEBAPOLLO_REMOTE_USER_AUTH") ?: false
+        ],
+        [
+            "name":"Username Password Authenticator",
+            "className":"usernamePasswordAuthenticatorService",
+            "active": System.getenv("WEBAPOLLO_USER_PASSWORD_AUTH") ?: true
+        ]
+    ]
 }
 
 jbrowse {

docs/Setup.md

@@ -75,7 +75,6 @@ server `apollo run-local` or `apollo debug` use the development environment (i.e
 * `apollo test` uses the test environment (i.e. only when running unit tests)
 
 
-
 #### Configure for H2:
 - H2 is an embedded database engine, so no external setups are needed. Simply copy sample-h2-apollo-config.groovy to
   apollo-config.groovy.
@@ -88,21 +87,11 @@ server `apollo run-local` or `apollo debug` use the development environment (i.e
 - Copy the sample-postgres-apollo-config.groovy to apollo-config.groovy. 
 
 
-
 #### Configure for MySQL:
 - Create a new MySQL database for production mode (i.e. run ``create database `apollo-production``` in the mysql
   console) and copy the sample-postgres-apollo-config.groovy to apollo-config.groovy.
 
 
-#### Configure for Docker:
-- Set up and export all of the environment variables you wish to configure. At bare minimum you will likely wish to set
-  `WEBAPOLLO_DB_USERNAME`, `WEBAPOLLO_DB_PASSWORD`, `WEBAPOLLO_DB_DRIVER`, `WEBAPOLLO_DB_DIALECT`, and
-`WEBAPOLLO_DB_URI`
-- Create a new database in your chosen database backend and copy the sample-docker-apollo-config.groovy to
-  apollo-config.groovy.
-- [Instructions and a script for launching docker with apollo and PostgreSQL](https://github.com/GMOD/docker-apollo).
-
-
 #### Apollo in Galaxy
 Apollo can always be used externally from Galaxy, but there are a few integrations available as well.
 

docs/index.rst

@@ -8,7 +8,7 @@ Javascript client that runs in a web browser as a JBrowse plugin.
 
 You can find the latest release here: https://github.com/GMOD/Apollo/releases/latest and our setup guide: http://genomearchitect.readthedocs.io/en/latest/Setup.html
 
-- Apollo general documentation: `https://genomearchitect.github.io/ <https://genomearchitect.github.io>`__
+- Apollo general documentation: `http://genomearchitect.github.io/ <http://genomearchitect.github.io>`__
 
 - JBrowse general documentation: `http://jbrowse.org <http://jbrowse.org>`__
 

grails-app/conf/Config.groovy

@@ -402,8 +402,8 @@ auditLog {
 jbrowse {
     git {
         url = "https://github.com/gmod/jbrowse"
-		branch = "1.16.5-release"
-//        branch = "dev"
+        branch = "1.16.6-release"
+//		branch = "dev"
 //        tag = "15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
         alwaysPull = true
         alwaysRecheck = true

grails-app/views/auth/login.gsp

@@ -12,35 +12,12 @@
     <g:form action="signIn">
         <input type="hidden" name="targetUri" value="${targetUri}" class="col-md-4"/>
         <div class="col-md-5 col-lg-offset-1" style="margin-top: 10px;">
-            %{--<input type="username" class="form-control" placeholder="Username (email)" required autofocus>--}%
-            %{--<input type="password" class="form-control" placeholder="Password" required>--}%
-            %{--<button class="btn btn-lg btn-primary btn-block" type="submit">--}%
-            %{--Sign in</button>--}%
-            %{--<label class="checkbox pull-left">--}%
-            %{--<input type="checkbox" value="${rememberMe}">--}%
-            %{--Remember me--}%
-            %{--</label>--}%
-            %{--<table>--}%
-            %{--<tbody>--}%
-            %{--<tr>--}%
-            %{--<td>Username:</td>--}%
-            %{--<td>--}%
             <input name="username" value="${username}" type="username" class="form-control col-md-4"
                    style="margin:10px;"
                    placeholder="Username (email)"
                    required autofocus/>
-            %{--</td>--}%
-            %{--</tr>--}%
-            %{--<tr>--}%
-            %{--<td>Password:</td>--}%
-            %{--<td><input type="password" name="password" value="" /></td>--}%
             <input type="password" name="password" value="" class="form-control" placeholder="Password" required
                    style="margin:10px;"/>
-            %{--</tr>--}%
-            %{--<tr>--}%
-            %{--<td>Remember me?:</td>--}%
-            %{--<td><g:checkBox name="rememberMe" value="${rememberMe}" /></td>--}%
-            %{--<div class="col-md-5 row" style="margin-bottom: 10px;">--}%
                 <input class="col-md-4 col-md-offset-1 btn btn-lg btn-primary" type="submit"
                        value="Login">
 
@@ -49,19 +26,6 @@
                     <input class="checkbox" type="checkbox" name="rememberMe" value="${rememberMe}"/>
                     Remember me
                 </label>
-            %{--</div>--}%
-
-            %{--<div class="col-md-5 row">--}%
-            %{--</div>--}%
-            %{--</tr>--}%
-            %{--<tr>--}%
-            %{--<td />--}%
-            %{--<input type="submit" value="Sign in"/>--}%
-            %{--<button class="btn btn-lg btn-primary btn-block" type="submit" value="Login">--}%
-            %{--<td><input type="submit" value="Sign in" /></td>--}%
-            %{--</tr>--}%
-            %{--</tbody>--}%
-            %{--</table>--}%
         </div>
     </g:form>
 </body>

src/gwt/org/bbop/apollo/gwt/client/Annotator.java

@@ -91,6 +91,11 @@ public void onResponseReceived(Request request, Response response) {
                             if(statusCode==200 && response.getText().equals("{}")){
                                 GWT.log("Still connected");
                             }
+                            else
+                            if(statusCode==200 && response.getText().contains("/apollo/auth/signIn")){
+                                GWT.log("Back up and trying to login");
+                                Window.Location.reload();
+                            }
                             else{
                                 if(!confirmOpen){
                                     confirmOpen = true ;

src/gwt/org/bbop/apollo/gwt/client/GroupPanel.java

@@ -40,7 +40,6 @@
 import org.gwtbootstrap3.extras.bootbox.client.callback.ConfirmCallback;
 import org.gwtbootstrap3.extras.select.client.ui.MultipleSelect;
 import org.gwtbootstrap3.extras.select.client.ui.Option;
-import org.gwtbootstrap3.extras.select.client.ui.Select;
 
 import java.util.ArrayList;
 import java.util.Comparator;
@@ -92,9 +91,14 @@ interface UserGroupBrowserPanelUiBinder extends UiBinder<Widget, GroupPanel> {
     MultipleSelect availableGroupAdmin;
     @UiField
     Button updateGroupAdmin;
+    @UiField
+    static TextBox nameSearchBox;
+
+    static private ListDataProvider<GroupInfo> dataProvider = new ListDataProvider<>();
+    private static List<GroupInfo> groupInfoList = new ArrayList<>();
+    private static List<GroupInfo> filteredGroupInfoList = dataProvider.getList();
+
 
-    private ListDataProvider<GroupInfo> dataProvider = new ListDataProvider<>();
-    private List<GroupInfo> groupInfoList = dataProvider.getList();
     private SingleSelectionModel<GroupInfo> selectionModel = new SingleSelectionModel<>();
     private GroupInfo selectedGroupInfo;
     private ColumnSortEvent.ListHandler<GroupInfo> groupSortHandler = new ColumnSortEvent.ListHandler<>(groupInfoList);
@@ -183,6 +187,7 @@ public void onGroupChanged(GroupChangeEvent userChangeEvent) {
                     case GROUPS_RELOADED:
                         selectedGroupInfo = null;
                         selectionModel.clear();
+                        filterList();
                         break;
 
 
@@ -194,7 +199,7 @@ public void onGroupChanged(GroupChangeEvent userChangeEvent) {
             @Override
             public boolean execute() {
                 if (MainPanel.getInstance().getCurrentUser() != null) {
-                    if(MainPanel.getInstance().isCurrentUserInstructorOrBetter())  {
+                    if (MainPanel.getInstance().isCurrentUserInstructorOrBetter()) {
                         GroupRestService.loadGroups(groupInfoList);
                         UserRestService.loadUsers(allUsersList);
                     }
@@ -441,6 +446,24 @@ public void reload() {
         }
     }
 
+    @UiHandler("nameSearchBox")
+    public void doSearch(KeyUpEvent keyUpEvent) {
+        filterList();
+    }
+
+    static void filterList() {
+        String text = nameSearchBox.getText();
+        filteredGroupInfoList.clear();
+        if (text.trim().length() == 0) {
+            filteredGroupInfoList.addAll(groupInfoList);
+            return;
+        }
+        for (GroupInfo groupInfo : groupInfoList) {
+            if (groupInfo.getName().toLowerCase().contains(text.toLowerCase())) {
+                filteredGroupInfoList.add(groupInfo);
+            }
+        }
+    }
 
     private void createOrganismPermissionsTable() {
         TextColumn<GroupOrganismPermissionInfo> organismNameColumn = new TextColumn<GroupOrganismPermissionInfo>() {

src/gwt/org/bbop/apollo/gwt/client/GroupPanel.ui.xml

@@ -52,6 +52,9 @@
         <gwt:north size="40">
             <b:Container fluid="true" width="100%">
                 <b:Row styleName="{style.northPanel}">
+                    <b:Column size="MD_4">
+                        <b:TextBox placeholder="Search" ui:field="nameSearchBox"/>
+                    </b:Column>
                     <b:Column size="MD_4">
                         <b:Button ui:field="createButton" icon="PLUS">Add Group</b:Button>
                         <b:Button ui:field="saveButton" icon="SAVE" visible="false" type="PRIMARY">Save</b:Button>

src/gwt/org/bbop/apollo/gwt/client/OrganismPanel.java

@@ -2,10 +2,7 @@
 
 import com.google.gwt.cell.client.NumberCell;
 import com.google.gwt.core.client.GWT;
-import com.google.gwt.event.dom.client.ChangeEvent;
-import com.google.gwt.event.dom.client.ClickEvent;
-import com.google.gwt.event.dom.client.DoubleClickEvent;
-import com.google.gwt.event.dom.client.DoubleClickHandler;
+import com.google.gwt.event.dom.client.*;
 import com.google.gwt.http.client.Request;
 import com.google.gwt.http.client.RequestCallback;
 import com.google.gwt.http.client.Response;
@@ -38,6 +35,7 @@
 import org.gwtbootstrap3.extras.bootbox.client.Bootbox;
 import org.gwtbootstrap3.extras.bootbox.client.callback.ConfirmCallback;
 
+import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.List;
 
@@ -113,14 +111,20 @@ interface OrganismBrowserPanelUiBinder extends UiBinder<Widget, OrganismPanel> {
     TextBox organismUploadSpecies;
     @UiField
     TextBox organismUploadNonDefaultTranslationTable;
+    @UiField
+    static TextBox nameSearchBox;
 
     boolean creatingNewOrganism = false; // a special flag for handling the clearSelection event when filling out new organism info
     boolean savingNewOrganism = false; // a special flag for handling the clearSelection event when filling out new organism info
 
     final LoadingDialog loadingDialog;
     final ErrorDialog errorDialog;
-    private ListDataProvider<OrganismInfo> dataProvider = new ListDataProvider<>();
-    private List<OrganismInfo> organismInfoList = dataProvider.getList();
+
+    static private ListDataProvider<OrganismInfo> dataProvider = new ListDataProvider<>();
+    private static List<OrganismInfo> organismInfoList = new ArrayList<>();
+    private static List<OrganismInfo> filteredOrganismInfoList = dataProvider.getList();
+
+
     private final SingleSelectionModel<OrganismInfo> singleSelectionModel = new SingleSelectionModel<>();
 
     public OrganismPanel() {
@@ -200,6 +204,7 @@ public Integer getValue(OrganismInfo object) {
             public void onOrganismChanged(OrganismChangeEvent organismChangeEvent) {
                 organismInfoList.clear();
                 organismInfoList.addAll(MainPanel.getInstance().getOrganismInfoList());
+                filterList();
             }
         });
 
@@ -274,6 +279,26 @@ public int compare(OrganismInfo o1, OrganismInfo o2) {
 
     }
 
+
+    @UiHandler("nameSearchBox")
+    public void doSearch(KeyUpEvent keyUpEvent) {
+        filterList();
+    }
+
+    static void filterList() {
+        String text = nameSearchBox.getText();
+        filteredOrganismInfoList.clear();
+        if(text.trim().length()==0){
+            filteredOrganismInfoList.addAll(organismInfoList);
+            return ;
+        }
+        for (OrganismInfo organismInfo : organismInfoList) {
+            if (organismInfo.getName().toLowerCase().contains(text.toLowerCase())) {
+                    filteredOrganismInfoList.add(organismInfo);
+            }
+        }
+    }
+
     public void loadOrganismInfo() {
         loadOrganismInfo(singleSelectionModel.getSelectedObject());
     }