Merge 20.3.1 to 20.4

panoramapublic/test/src/org/labkey/test/categories/MacCossLabModules.java

@@ -0,0 +1,5 @@
+package org.labkey.test.categories;
+
+public abstract class MacCossLabModules extends Weekly
+{
+}

panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicTest.java

@@ -7,8 +7,8 @@
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.TestTimeoutException;
-import org.labkey.test.categories.DailyB;
-import org.labkey.test.categories.MS2;
+import org.labkey.test.categories.External;
+import org.labkey.test.categories.MacCossLabModules;
 import org.labkey.test.components.BodyWebPart;
 import org.labkey.test.components.CustomizeView;
 import org.labkey.test.pages.InsertPage;
@@ -24,7 +24,7 @@
 
 import static org.junit.Assert.assertEquals;
 
-@Category({DailyB.class, MS2.class})
+@Category({External.class, MacCossLabModules.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class PanoramaPublicTest extends TargetedMSTest implements PostgresOnlyTest
 {

passport/test/src/org/labkey/test/tests/passport/PassportTest.java

@@ -19,14 +19,15 @@
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.test.Locator;
-import org.labkey.test.categories.CustomModules;
+import org.labkey.test.categories.External;
+import org.labkey.test.categories.MacCossLabModules;
 import org.labkey.test.util.LogMethod;
 import org.labkey.test.util.PostgresOnlyTest;
 import org.labkey.test.util.UIContainerHelper;
 
 import java.util.List;
 
-@Category({CustomModules.class})
+@Category({External.class, MacCossLabModules.class})
 public class PassportTest  extends PassportTestPart implements PostgresOnlyTest
 {
     public PassportTest()

pwebdashboard/build.gradle

@@ -0,0 +1,6 @@
+import org.labkey.gradle.util.BuildUtils;
+
+dependencies {
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:targetedms", depProjectConfig: "apiJarFile")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:targetedms", depProjectConfig: "published", depExtension: "module")
+}

pwebdashboard/module.properties

@@ -0,0 +1,8 @@
+Name: PanoramaWeb Dashboard
+ModuleClass: org.labkey.pwebdashboard.PwebDashboardModule
+Label: PanoramaWeb Dashboard
+Description: Queries and code to render PanoramaWeb usage charts.
+URL: https://panoramaweb.org/wiki/home/page.view?name=Dashboard
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+SupportedDatabases: pgsql

pwebdashboard/resources/queries/pwebdashboard/ProjectDetails.sql

@@ -0,0 +1,7 @@
+SELECT FolderDocs.Project,
+SUM(FolderDocs.Documents) AS TotalDocs,
+SUM((CASE WHEN FolderDocs.TargetedMSFolderType='Experiment' OR FolderDocs.TargetedMSFolderType IS NULL THEN FolderDocs.Documents ELSE 0 END)) AS ExpDocs,
+SUM((CASE WHEN FolderDocs.TargetedMSFolderType='Library' OR FolderDocs.TargetedMSFolderType='LibraryProtein' THEN FolderDocs.Documents ELSE 0 END)) AS LibDocs,
+SUM((CASE WHEN FolderDocs.TargetedMSFolderType='QC' THEN FolderDocs.Documents ELSE 0 END)) AS QcDocs,
+MAX(FolderDocs.LastUpload) AS LastUpload
+FROM FolderDocs GROUP BY FolderDocs.Project

pwebdashboard/src/org/labkey/pwebdashboard/FolderDocsTable.java

@@ -0,0 +1,98 @@
+package org.labkey.pwebdashboard;
+
+import org.jetbrains.annotations.NotNull;
+import org.labkey.api.data.BaseColumnInfo;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerForeignKey;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.ContainerTable;
+import org.labkey.api.data.CoreSchema;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.WrappedColumn;
+import org.labkey.api.query.ExprColumn;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.targetedms.TargetedMSService;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Created by vsharma on 12/8/2016.
+ */
+public class FolderDocsTable extends ContainerTable
+{
+    public static final String NAME = "FolderDocs";
+
+    public FolderDocsTable(@NotNull PwebDashboardSchema userSchema, ContainerFilter cf)
+    {
+        super(userSchema, cf);
+
+        setName(NAME);
+
+        BaseColumnInfo folderCol = new WrappedColumn(getColumn("EntityId"), "Folder");
+        ContainerForeignKey.initColumn(folderCol, userSchema);
+        addColumn(folderCol);
+
+        /*
+        WITH RECURSIVE project(parent, entityId, name) AS (
+        SELECT parent, entityId, name FROM core.containers WHERE name='QC Subfolder 2a'
+        UNION
+        SELECT a.parent AS parent, p.parent AS entityId, a.name AS name FROM project p, core.containers a
+        WHERE a.entityId = p.parent
+        ) SELECT * FROM project WHERE parent = (SELECT entityId FROM core.containers WHERE parent IS NULL)
+         */
+        // Get the project for the folder. Traverse up the folder tree.
+        SQLFragment projectColSql = new SQLFragment("(WITH RECURSIVE project(parent, entityId, name) AS ( ");
+        projectColSql.append(" SELECT parent, entityId, name FROM ").append(CoreSchema.getInstance().getTableInfoContainers(), "c");
+        projectColSql.append(" WHERE entityId=").append(ExprColumn.STR_TABLE_ALIAS).append(".EntityId");
+        projectColSql.append(" UNION ");
+        projectColSql.append(" SELECT a.parent AS parent, p.parent AS entityId, a.name AS name FROM project p, core.containers a WHERE a.entityId = p.parent ");
+        projectColSql.append(" ) SELECT entityId FROM project WHERE parent = ?)");
+        projectColSql.add(ContainerManager.getRoot().getEntityId());
+        ExprColumn projectCol = new ExprColumn(this, "Project", projectColSql, JdbcType.VARCHAR);
+        projectCol.setReadOnly(true);
+        ContainerForeignKey.initColumn(projectCol, userSchema);
+        addColumn(projectCol);
+
+        TargetedMSService tmsService = TargetedMSService.get();
+
+        SQLFragment docCountSql = new SQLFragment(" (SELECT COUNT(*) FROM ");
+        docCountSql.append(tmsService.getTableInfoRuns(), "r");
+        docCountSql.append(" WHERE container=").append(ExprColumn.STR_TABLE_ALIAS).append(".EntityId");
+        docCountSql.append(" AND deleted = FALSE AND statusId=1) ");
+        ExprColumn documentCountCol = new ExprColumn(this, "Documents", docCountSql, JdbcType.INTEGER);
+        addColumn(documentCountCol);
+
+        SQLFragment lastUploadSql = new SQLFragment(" (SELECT MAX(Created) FROM ");
+        lastUploadSql.append(tmsService.getTableInfoRuns(), "r");
+        lastUploadSql.append(" WHERE container=").append(ExprColumn.STR_TABLE_ALIAS).append(".EntityId");
+        lastUploadSql.append(" AND deleted = FALSE AND statusId=1) ");
+        ExprColumn lastUploadCol = new ExprColumn(this, "LastUpload", lastUploadSql, JdbcType.DATE);
+        addColumn(lastUploadCol);
+
+        SQLFragment folderTypeColSql = new SQLFragment(" (SELECT p.value FROM prop.properties AS p INNER JOIN prop.propertySets AS ps ON p.set = ps.set ");
+        folderTypeColSql.append(" WHERE p.Name=?");
+        folderTypeColSql.add(tmsService.FOLDER_TYPE_PROP_NAME);
+        folderTypeColSql.append(" AND ps.category=?");
+        folderTypeColSql.add("moduleProperties." + tmsService.MODULE_NAME);
+        folderTypeColSql.append(" AND ps.ObjectId=").append(ExprColumn.STR_TABLE_ALIAS).append(".EntityId");
+        folderTypeColSql.append(") ");
+        ExprColumn folderTypeCol = new ExprColumn(this, "TargetedMSFolderType", folderTypeColSql, JdbcType.VARCHAR);
+        addColumn(folderTypeCol);
+
+
+        List<FieldKey> visibleColumns = new ArrayList<>();
+        visibleColumns.add(FieldKey.fromParts("Project"));
+        visibleColumns.add(FieldKey.fromParts("Created"));
+        visibleColumns.add(FieldKey.fromParts("CreatedBy"));
+        visibleColumns.add(FieldKey.fromParts("Folder"));
+        visibleColumns.add(FieldKey.fromParts("TargetedMSFolderType"));
+        visibleColumns.add(FieldKey.fromParts("Documents"));
+        visibleColumns.add(FieldKey.fromParts("LastUpload"));
+        setDefaultVisibleColumns(visibleColumns);
+
+        SQLFragment sql = new SQLFragment("(CreatedBy IS NOT NULL)");
+        addCondition(sql);
+    }
+}