Make it possible for users to view their data on Panorama Public (#387)

Add a "My Data" view for datasets submitted to Panorama Public.

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java

@@ -178,6 +178,7 @@
 import org.labkey.panoramapublic.query.ExperimentAnnotationsManager;
 import org.labkey.panoramapublic.query.JournalManager;
 import org.labkey.panoramapublic.query.ModificationInfoManager;
+import org.labkey.panoramapublic.query.MyDataTableInfo;
 import org.labkey.panoramapublic.query.PxXmlManager;
 import org.labkey.panoramapublic.query.SpecLibInfoManager;
 import org.labkey.panoramapublic.query.SubmissionManager;
@@ -8952,7 +8953,7 @@ public ModelAndView getView(IdForm form, BindException errors)
 
             ensureCorrectContainer(getContainer(), expAnnotations.getContainer(), getViewContext()); // container check
 
-            return new CatalogEntryWebPart(expAnnotations, getUser(), true);
+            return new CatalogEntryWebPart(expAnnotations, getUser(), form.getReturnActionURL(PageFlowUtil.urlProvider(ProjectUrls.class).getBeginURL(getContainer())));
         }
 
         @Override
@@ -9183,6 +9184,34 @@ public ModelAndView getView(Object o, BindException errors)
         }
     }
 
+    @RequiresPermission(ReadPermission.class)
+    @RequiresLogin
+    public class MyDataViewAction extends SimpleViewAction<Object>
+    {
+        @Override
+        public void addNavTrail(NavTree root)
+        {
+            root.addChild("My Panorama Public Data");
+        }
+
+        @Override
+        public ModelAndView getView(Object o, BindException errors) throws Exception
+        {
+            QuerySettings settings = new QuerySettings(getViewContext(),  MyDataTableInfo.NAME, MyDataTableInfo.NAME);
+            settings.setContainerFilterName(ContainerFilter.Type.CurrentAndSubfolders.name());
+            QueryView view = new QueryView(new PanoramaPublicSchema(getUser(), getContainer()), settings, errors);
+            view.setTitle("Panorama Public Experiments");
+            view.setShowRecordSelectors(false);
+            view.setShowExportButtons(false);
+            view.setShowDetailsColumn(false);
+            view.setShowDeleteButton(false);
+            view.setShowUpdateColumn(false);
+            view.setShowInsertNewButton(false);
+            view.disableContainerFilterSelection();
+            return view;
+        }
+    }
+
     // ------------------------------------------------------------------------
     // BEGIN Assign PanoramaPublicSubmitterRole to data submitters and lab heads
     // ------------------------------------------------------------------------

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicSchema.java

@@ -54,6 +54,7 @@
 import org.labkey.panoramapublic.query.DataValidationTableInfo;
 import org.labkey.panoramapublic.query.ExperimentAnnotationsTableInfo;
 import org.labkey.panoramapublic.query.JournalExperimentTableInfo;
+import org.labkey.panoramapublic.query.MyDataTableInfo;
 import org.labkey.panoramapublic.query.PanoramaPublicTable;
 import org.labkey.panoramapublic.query.SubmissionTableInfo;
 import org.labkey.panoramapublic.query.modification.ExperimentIsotopeModInfoTableInfo;
@@ -129,6 +130,10 @@ public TableInfo createTable(String name, ContainerFilter cf)
         {
             return new ExperimentAnnotationsTableInfo(this, cf);
         }
+        if (MyDataTableInfo.NAME.equalsIgnoreCase(name))
+        {
+            return new MyDataTableInfo(this, cf, getUser());
+        }
         if (TABLE_JOURNAL_EXPERIMENT.equalsIgnoreCase(name))
         {
             return new JournalExperimentTableInfo(this, cf);

panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java

@@ -53,6 +53,7 @@
 import org.labkey.api.security.roles.ProjectAdminRole;
 import org.labkey.api.security.roles.Role;
 import org.labkey.api.security.roles.RoleManager;
+import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.DOM;
 import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.PageFlowUtil;
@@ -65,8 +66,10 @@
 import org.labkey.panoramapublic.PanoramaPublicController;
 import org.labkey.panoramapublic.PanoramaPublicManager;
 import org.labkey.panoramapublic.PanoramaPublicSchema;
+import org.labkey.panoramapublic.model.CatalogEntry;
 import org.labkey.panoramapublic.model.DataLicense;
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
+import org.labkey.panoramapublic.view.publish.CatalogEntryWebPart;
 import org.labkey.panoramapublic.view.publish.ShortUrlDisplayColumnFactory;
 
 import java.io.IOException;
@@ -75,8 +78,12 @@
 import java.util.List;
 import java.util.Set;
 
+import static org.labkey.api.util.DOM.Attribute.height;
+import static org.labkey.api.util.DOM.Attribute.href;
 import static org.labkey.api.util.DOM.Attribute.onclick;
 import static org.labkey.api.util.DOM.Attribute.src;
+import static org.labkey.api.util.DOM.Attribute.title;
+import static org.labkey.api.util.DOM.Attribute.width;
 import static org.labkey.api.util.DOM.IMG;
 import static org.labkey.api.util.DOM.at;
 
@@ -337,6 +344,10 @@ public Class getDisplayValueClass()
         getMutableColumn("CreatedBy").setFk(new UserIdQueryForeignKey(schema));
         getMutableColumn("ModifiedBy").setFk(new UserIdQueryForeignKey(schema));
 
+        ExprColumn catalogEntryCol = getCatalogEntryCol();
+        catalogEntryCol.setDisplayColumnFactory(colInfo -> new CatalogEntryIconColumn(colInfo));
+        addColumn(catalogEntryCol);
+
         List<FieldKey> visibleColumns = new ArrayList<>();
         visibleColumns.add(FieldKey.fromParts("Share"));
         visibleColumns.add(FieldKey.fromParts("Title"));
@@ -407,6 +418,18 @@ private ExprColumn getVersionCountCol()
         return versionCountCol;
     }
 
+    private ExprColumn getCatalogEntryCol()
+    {
+        SQLFragment catalogEntrySql = new SQLFragment(" (SELECT entry.id AS CatalogEntry ")
+                .append(" FROM ").append(PanoramaPublicManager.getTableInfoCatalogEntry(), "entry")
+                .append(" WHERE ")
+                .append(" entry.shortUrl = ").append(ExprColumn.STR_TABLE_ALIAS).append(".shortUrl")
+                .append(") ");
+        ExprColumn col = new ExprColumn(this, "CatalogEntry", catalogEntrySql, JdbcType.INTEGER);
+        col.setDescription("Add or view the catalog entry for the experiment");
+        return col;
+    }
+
     @Override
     public String getName()
     {
@@ -724,4 +747,48 @@ String getRenderId()
             return "input-picker-div-instrument";
         }
     }
+
+    public static class CatalogEntryIconColumn extends DataColumn
+    {
+        public CatalogEntryIconColumn(ColumnInfo col)
+        {
+            super(col);
+            super.setCaption("Catalog Entry");
+        }
+
+        @Override
+        public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
+        {
+            User user = ctx.getViewContext().getUser();
+            if (user == null || user.isGuest())
+            {
+                HtmlString.NBSP.appendTo(out);
+                return;
+            }
+            Integer catalogEntryId = ctx.get(getColumnInfo().getFieldKey(), Integer.class);
+
+            // Get the experiment connected with this catalog entry.
+            Integer experimentId = ctx.get(FieldKey.fromParts("id"), Integer.class);
+            if (experimentId != null)
+            {
+                ExperimentAnnotations expAnnot = ExperimentAnnotationsManager.get(experimentId);
+                // Display the catalog entry link only if the user has the required permissions (Admin or PanoramaPublicSubmitter) in the the experiment folder.
+                if (expAnnot != null && CatalogEntryWebPart.canBeDisplayed(expAnnot, user))
+                {
+                    CatalogEntry entry = catalogEntryId == null ? null : CatalogEntryManager.get(catalogEntryId);
+                    String imageUrl = entry != null ? AppProps.getInstance().getContextPath() + "/PanoramaPublic/images/slideshow-icon-green.png"
+                                                    : AppProps.getInstance().getContextPath() + "/PanoramaPublic/images/slideshow-icon.png";
+                    String imageTitle = entry != null ? "View catalog entry" : "Add catalog entry";
+                    ActionURL returnUrl = ctx.getViewContext().getActionURL().clone();
+                    ActionURL catalogEntryLink = entry != null ? PanoramaPublicController.getViewCatalogEntryUrl(expAnnot, entry).addReturnURL(returnUrl)
+                                                               : PanoramaPublicController.getAddCatalogEntryUrl(expAnnot).addReturnURL(returnUrl);
+                    DOM.A(at(href, catalogEntryLink.getLocalURIString(), title, PageFlowUtil.filter(imageTitle)),
+                            DOM.IMG(at(src, imageUrl, height, 22, width, 22)))
+                            .appendTo(out);
+                    return;
+                }
+            }
+            HtmlString.NBSP.appendTo(out);
+        }
+    }
 }

panoramapublic/src/org/labkey/panoramapublic/query/MyDataTableInfo.java

@@ -0,0 +1,45 @@
+package org.labkey.panoramapublic.query;
+
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.security.User;
+import org.labkey.panoramapublic.PanoramaPublicSchema;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class MyDataTableInfo extends ExperimentAnnotationsTableInfo
+{
+    public static final String NAME = "MyPanoramaPublicData";
+
+    public MyDataTableInfo(PanoramaPublicSchema schema, ContainerFilter cf, User user)
+    {
+        super(schema, cf);
+
+        if (user != null)
+        {
+            // Filter to rows where the given user is either the submitter or the lab head.
+            SimpleFilter.OrClause or = new SimpleFilter.OrClause();
+            or.addClause(new CompareType.EqualsCompareClause(FieldKey.fromParts("submitter"), CompareType.EQUAL, user.getUserId()));
+            or.addClause(new CompareType.EqualsCompareClause(FieldKey.fromParts("labhead"), CompareType.EQUAL, user.getUserId()));
+            SimpleFilter filter = new SimpleFilter();
+            filter.addClause(or);
+            addCondition(filter);
+        }
+
+        List<FieldKey> visibleColumns = new ArrayList<>();
+        visibleColumns.add(FieldKey.fromParts("Share"));
+        visibleColumns.add(FieldKey.fromParts("Title"));
+        visibleColumns.add(FieldKey.fromParts("Organism"));
+        visibleColumns.add(FieldKey.fromParts("Instrument"));
+        visibleColumns.add(FieldKey.fromParts("Runs"));
+        visibleColumns.add(FieldKey.fromParts("Keywords"));
+        visibleColumns.add(FieldKey.fromParts("Citation"));
+        visibleColumns.add(FieldKey.fromParts("pxid"));
+        visibleColumns.add(FieldKey.fromParts("Public"));
+        visibleColumns.add(FieldKey.fromParts("CatalogEntry"));
+        setDefaultVisibleColumns(visibleColumns);
+    }
+}

panoramapublic/src/org/labkey/panoramapublic/view/expannotations/TargetedMSExperimentsWebPart.java

@@ -77,5 +77,12 @@ protected void populateButtonBar(DataView view, ButtonBar bb)
         deleteExperimentAnnotation.setDisplayPermission(DeletePermission.class);
         deleteExperimentAnnotation.setRequiresSelection(true);
         bb.add(deleteExperimentAnnotation);
+
+        if (!view.getViewContext().getUser().isGuest())
+        {
+            ActionURL viewMyDataUrl = new ActionURL(PanoramaPublicController.MyDataViewAction.class, getContainer());
+            ActionButton viewMyDataButton = new ActionButton(viewMyDataUrl, "My Data");
+            bb.add(viewMyDataButton);
+        }
     }
 }

panoramapublic/src/org/labkey/panoramapublic/view/publish/CatalogEntryWebPart.java

@@ -1,13 +1,11 @@
 package org.labkey.panoramapublic.view.publish;
 
-import org.labkey.api.action.UrlProvider;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
-import org.labkey.api.portal.ProjectUrls;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.AdminPermission;
 import org.labkey.api.util.Button;
 import org.labkey.api.util.HtmlString;
-import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.HtmlView;
@@ -40,10 +38,10 @@ public class CatalogEntryWebPart extends VBox
 {
     public CatalogEntryWebPart(ExperimentAnnotations expAnnotations, User user)
     {
-        this(expAnnotations, user, false);
+        this(expAnnotations, user, null);
     }
 
-    public CatalogEntryWebPart(ExperimentAnnotations expAnnotations, User user, boolean standalone)
+    public CatalogEntryWebPart(ExperimentAnnotations expAnnotations, User user, @Nullable ActionURL returnUrl)
     {
         Container container = expAnnotations.getContainer();
         setTitle("Panorama Public Catalog Entry");
@@ -108,9 +106,8 @@ public CatalogEntryWebPart(ExperimentAnnotations expAnnotations, User user, bool
                     HtmlString.NBSP,
                     new Button.ButtonBuilder("Delete").href(deleteUrl)
                             .usePost("Are you sure you want to delete the Panorama Public catalog entry for this experiment?"),
-                    standalone ? DIV(at(style, "margin-top:25px;"),
-                                     new Button.ButtonBuilder("Back to Folder").href(PageFlowUtil.urlProvider(ProjectUrls.class).getBeginURL(container)))
-                               : HtmlString.EMPTY_STRING
+                    returnUrl != null ? DIV(at(style, "margin-top:25px;"), new Button.ButtonBuilder("Back").href(returnUrl))
+                                      : HtmlString.EMPTY_STRING
             )));
         }
     }

panoramapublic/src/org/labkey/panoramapublic/view/publish/catalogEntryForm.jsp

@@ -53,7 +53,7 @@
     int imgWidth = settings.getImgWidth();
     int imgHeight = settings.getImgHeight();
 
-    ActionURL cancelUrl = PanoramaPublicController.getViewExperimentDetailsURL(form.getId(), form.getContainer());
+    ActionURL cancelUrl = bean.getForm().getReturnActionURL(PanoramaPublicController.getViewExperimentDetailsURL(form.getId(), form.getContainer()));
 
 %>
 <labkey:errors/>

panoramapublic/src/org/labkey/panoramapublic/view/search/panoramaWebSearch.jsp

@@ -479,6 +479,16 @@
                     success: function (wp) {
                         let expWebpart = wp.body.filter(webpart => webpart.name === "Targeted MS Experiment List");
                         if (expWebpart.length === 1) {
+
+                            let buttonBarItems = [];
+                            if (!LABKEY.user.isGuest)
+                            {
+                                buttonBarItems = [
+                                    {text: 'My Data', url: LABKEY.ActionURL.buildURL('panoramapublic', 'myDataView')},
+                                    LABKEY.QueryWebPart.standardButtons.views
+                               ];
+                            }
+
                             let wp = new LABKEY.QueryWebPart({
                                 renderTo: 'webpart_'+ expWebpart[0].webPartId,
                                 title: 'Panorama Public Experiments',
@@ -491,6 +501,10 @@
                                 showExportButtons: false,//this needs to be set to false otherwise setting selectRecordSelector to false still shows the checkbox column
                                 showDetailsColumn: false,
                                 dataRegionName: "Targeted MS Experiment List",
+                                buttonBar: {
+                                    includeStandardButtons: true,
+                                    items: buttonBarItems,
+                                },
                                 success: function () {
                                 }
                             });

panoramapublic/test/src/org/labkey/test/components/panoramapublic/TargetedMsExperimentWebPart.java

@@ -43,7 +43,7 @@ public TargetedMsExperimentInsertPage startInsert()
 
     public void clickSubmit()
     {
-        getWrapper().clickAndWait(Locator.linkContainingText("Submit"));
+        getWrapper().clickAndWait(Locator.linkWithText("Submit"));
     }
 
     public void clickResubmit()