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/*
* Copyright (c) 2008-2019 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.labkey.query.controllers;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.genai.Chat;
import com.google.genai.errors.ClientException;
import com.google.genai.errors.ServerException;
import jakarta.servlet.ServletException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import jakarta.servlet.http.HttpSession;
import org.antlr.runtime.tree.Tree;
import org.apache.commons.beanutils.ConversionException;
import org.apache.commons.beanutils.ConvertUtils;
import org.apache.commons.collections4.MultiValuedMap;
import org.apache.commons.collections4.multimap.ArrayListValuedHashMap;
import org.apache.commons.collections4.multimap.HashSetValuedHashMap;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.apache.commons.lang3.mutable.MutableInt;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.xmlbeans.XmlError;
import org.apache.xmlbeans.XmlException;
import org.apache.xmlbeans.XmlOptions;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.json.JSONParserConfiguration;
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.labkey.api.action.Action;
import org.labkey.api.action.ActionType;
import org.labkey.api.action.ApiJsonForm;
import org.labkey.api.action.ApiJsonWriter;
import org.labkey.api.action.ApiQueryResponse;
import org.labkey.api.action.ApiResponse;
import org.labkey.api.action.ApiResponseWriter;
import org.labkey.api.action.ApiSimpleResponse;
import org.labkey.api.action.ApiUsageException;
import org.labkey.api.action.ApiVersion;
import org.labkey.api.action.ConfirmAction;
import org.labkey.api.action.ExportAction;
import org.labkey.api.action.ExportException;
import org.labkey.api.action.ExtendedApiQueryResponse;
import org.labkey.api.action.FormHandlerAction;
import org.labkey.api.action.FormViewAction;
import org.labkey.api.action.HasBindParameters;
import org.labkey.api.action.JsonInputLimit;
import org.labkey.api.action.LabKeyError;
import org.labkey.api.action.Marshal;
import org.labkey.api.action.Marshaller;
import org.labkey.api.action.MutatingApiAction;
import org.labkey.api.action.NullSafeBindException;
import org.labkey.api.action.ReadOnlyApiAction;
import org.labkey.api.action.ReportingApiQueryResponse;
import org.labkey.api.action.SimpleApiJsonForm;
import org.labkey.api.action.SimpleErrorView;
import org.labkey.api.action.SimpleRedirectAction;
import org.labkey.api.action.SimpleViewAction;
import org.labkey.api.action.SpringActionController;
import org.labkey.api.admin.AdminUrls;
import org.labkey.api.attachments.SpringAttachmentFile;
import org.labkey.api.audit.AbstractAuditTypeProvider;
import org.labkey.api.audit.AuditLogService;
import org.labkey.api.audit.AuditTypeEvent;
import org.labkey.api.audit.TransactionAuditProvider;
import org.labkey.api.audit.provider.ContainerAuditProvider;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.collections.CaseInsensitiveHashSet;
import org.labkey.api.collections.IntHashMap;
import org.labkey.api.collections.LabKeyCollectors;
import org.labkey.api.collections.RowMapFactory;
import org.labkey.api.collections.Sets;
import org.labkey.api.data.AbstractTableInfo;
import org.labkey.api.data.ActionButton;
import org.labkey.api.data.Aggregate;
import org.labkey.api.data.AnalyticsProviderItem;
import org.labkey.api.data.BaseColumnInfo;
import org.labkey.api.data.ButtonBar;
import org.labkey.api.data.CachedResultSetBuilder;
import org.labkey.api.data.ColumnHeaderType;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.ContainerType;
import org.labkey.api.data.DataRegion;
import org.labkey.api.data.DataRegionSelection;
import org.labkey.api.data.DbSchema;
import org.labkey.api.data.DbSchemaType;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.DisplayColumn;
import org.labkey.api.data.ExcelWriter;
import org.labkey.api.data.ForeignKey;
import org.labkey.api.data.JdbcMetaDataSelector;
import org.labkey.api.data.JdbcType;
import org.labkey.api.data.JsonWriter;
import org.labkey.api.data.PHI;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.PropertyMap;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.data.PropertyStorageSpec;
import org.labkey.api.data.QueryLogging;
import org.labkey.api.data.ResultSetView;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SchemaTableInfo;
import org.labkey.api.data.ShowRows;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.SqlExecutor;
import org.labkey.api.data.SqlSelector;
import org.labkey.api.data.TSVWriter;
import org.labkey.api.data.Table;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TableSelector;
import org.labkey.api.data.VirtualTable;
import org.labkey.api.data.dialect.JdbcMetaDataLocator;
import org.labkey.api.data.dialect.SqlDialect;
import org.labkey.api.dataiterator.DataIteratorBuilder;
import org.labkey.api.dataiterator.DataIteratorContext;
import org.labkey.api.dataiterator.DataIteratorUtil;
import org.labkey.api.dataiterator.DetailedAuditLogDataIterator;
import org.labkey.api.dataiterator.ListofMapsDataIterator;
import org.labkey.api.exceptions.OptimisticConflictException;
import org.labkey.api.exp.ExperimentException;
import org.labkey.api.exp.api.ProvenanceRecordingParams;
import org.labkey.api.exp.api.ProvenanceService;
import org.labkey.api.exp.list.ListDefinition;
import org.labkey.api.exp.list.ListService;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.exp.property.DomainAuditProvider;
import org.labkey.api.exp.property.DomainKind;
import org.labkey.api.exp.property.PropertyService;
import org.labkey.api.files.FileContentService;
import org.labkey.api.gwt.client.AuditBehaviorType;
import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
import org.labkey.api.mcp.AbstractAgentAction;
import org.labkey.api.mcp.McpContext;
import org.labkey.api.mcp.McpService;
import org.labkey.api.mcp.PromptForm;
import org.labkey.api.module.ModuleHtmlView;
import org.labkey.api.module.ModuleLoader;
import org.labkey.api.pipeline.RecordedAction;
import org.labkey.api.query.AbstractQueryImportAction;
import org.labkey.api.query.AbstractQueryUpdateService;
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.query.CustomView;
import org.labkey.api.query.DefaultSchema;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.DuplicateKeyException;
import org.labkey.api.query.ExportScriptModel;
import org.labkey.api.query.FieldKey;
import org.labkey.api.query.FilteredTable;
import org.labkey.api.query.InvalidKeyException;
import org.labkey.api.query.MetadataUnavailableException;
import org.labkey.api.query.QueryAction;
import org.labkey.api.query.QueryDefinition;
import org.labkey.api.query.QueryException;
import org.labkey.api.query.QueryForm;
import org.labkey.api.query.QueryParam;
import org.labkey.api.query.QueryParseException;
import org.labkey.api.query.QueryParseWarning;
import org.labkey.api.query.QuerySchema;
import org.labkey.api.query.QueryService;
import org.labkey.api.query.QuerySettings;
import org.labkey.api.query.QueryUpdateForm;
import org.labkey.api.query.QueryUpdateService;
import org.labkey.api.query.QueryUpdateServiceException;
import org.labkey.api.query.QueryUrls;
import org.labkey.api.query.QueryView;
import org.labkey.api.query.RuntimeValidationException;
import org.labkey.api.query.SchemaKey;
import org.labkey.api.query.SimpleSchemaTreeVisitor;
import org.labkey.api.query.TempQuerySettings;
import org.labkey.api.query.UserSchema;
import org.labkey.api.query.UserSchemaAction;
import org.labkey.api.query.ValidationException;
import org.labkey.api.reports.report.ReportDescriptor;
import org.labkey.api.security.ActionNames;
import org.labkey.api.security.AdminConsoleAction;
import org.labkey.api.security.CSRF;
import org.labkey.api.security.IgnoresTermsOfUse;
import org.labkey.api.security.MutableSecurityPolicy;
import org.labkey.api.security.RequiresAllOf;
import org.labkey.api.security.RequiresAnyOf;
import org.labkey.api.security.RequiresLogin;
import org.labkey.api.security.RequiresNoPermission;
import org.labkey.api.security.RequiresPermission;
import org.labkey.api.security.SecurityManager;
import org.labkey.api.security.SecurityPolicyManager;
import org.labkey.api.security.User;
import org.labkey.api.security.UserManager;
import org.labkey.api.security.ValidEmail;
import org.labkey.api.security.permissions.AbstractActionPermissionTest;
import org.labkey.api.security.permissions.AdminOperationsPermission;
import org.labkey.api.security.permissions.AdminPermission;
import org.labkey.api.security.permissions.DeletePermission;
import org.labkey.api.security.permissions.EditSharedViewPermission;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.security.permissions.MoveEntitiesPermission;
import org.labkey.api.security.permissions.Permission;
import org.labkey.api.security.permissions.PlatformDeveloperPermission;
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.security.permissions.UpdatePermission;
import org.labkey.api.security.roles.EditorRole;
import org.labkey.api.settings.AdminConsole;
import org.labkey.api.settings.AppProps;
import org.labkey.api.settings.LookAndFeelProperties;
import org.labkey.api.stats.BaseAggregatesAnalyticsProvider;
import org.labkey.api.stats.ColumnAnalyticsProvider;
import org.labkey.api.util.ButtonBuilder;
import org.labkey.api.util.ConfigurationException;
import org.labkey.api.util.DOM;
import org.labkey.api.util.ExceptionUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.HtmlStringBuilder;
import org.labkey.api.util.JavaScriptFragment;
import org.labkey.api.util.JsonUtil;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.util.ResponseHelper;
import org.labkey.api.util.ReturnURLString;
import org.labkey.api.util.SqlUtil;
import org.labkey.api.util.StringExpression;
import org.labkey.api.util.StringUtilsLabKey;
import org.labkey.api.util.TestContext;
import org.labkey.api.util.URLHelper;
import org.labkey.api.util.UnexpectedException;
import org.labkey.api.util.XmlBeansUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.DetailsView;
import org.labkey.api.view.HtmlView;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.InsertView;
import org.labkey.api.view.JspView;
import org.labkey.api.view.NavTree;
import org.labkey.api.view.NotFoundException;
import org.labkey.api.view.UnauthorizedException;
import org.labkey.api.view.UpdateView;
import org.labkey.api.view.VBox;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.ViewServlet;
import org.labkey.api.view.WebPartView;
import org.labkey.api.view.template.PageConfig;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.api.writer.ZipFile;
import org.labkey.data.xml.ColumnType;
import org.labkey.data.xml.ImportTemplateType;
import org.labkey.data.xml.TableType;
import org.labkey.data.xml.TablesDocument;
import org.labkey.data.xml.TablesType;
import org.labkey.data.xml.externalSchema.TemplateSchemaType;
import org.labkey.data.xml.queryCustomView.FilterType;
import org.labkey.query.AutoGeneratedDetailsCustomView;
import org.labkey.query.AutoGeneratedInsertCustomView;
import org.labkey.query.AutoGeneratedUpdateCustomView;
import org.labkey.query.CustomViewImpl;
import org.labkey.query.CustomViewUtil;
import org.labkey.query.EditQueriesPermission;
import org.labkey.query.EditableCustomView;
import org.labkey.query.LinkedTableInfo;
import org.labkey.query.MetadataTableJSON;
import org.labkey.query.ModuleCustomQueryDefinition;
import org.labkey.query.ModuleCustomView;
import org.labkey.query.QueryServiceImpl;
import org.labkey.query.TableXML;
import org.labkey.query.audit.QueryExportAuditProvider;
import org.labkey.query.audit.QueryUpdateAuditProvider;
import org.labkey.query.model.MetadataTableJSONMixin;
import org.labkey.query.persist.AbstractExternalSchemaDef;
import org.labkey.query.persist.CstmView;
import org.labkey.query.persist.ExternalSchemaDef;
import org.labkey.query.persist.ExternalSchemaDefCache;
import org.labkey.query.persist.LinkedSchemaDef;
import org.labkey.query.persist.QueryDef;
import org.labkey.query.persist.QueryManager;
import org.labkey.query.reports.ReportsController;
import org.labkey.query.reports.getdata.DataRequest;
import org.labkey.query.sql.QNode;
import org.labkey.query.sql.Query;
import org.labkey.query.sql.SqlParser;
import org.labkey.query.xml.ApiTestsDocument;
import org.labkey.query.xml.TestCaseType;
import org.labkey.remoteapi.RemoteConnections;
import org.labkey.remoteapi.SelectRowsStreamHack;
import org.labkey.remoteapi.query.SelectRowsCommand;
import org.labkey.vfs.FileLike;
import org.springframework.ai.chat.client.ChatClient;
import org.springframework.beans.MutablePropertyValues;
import org.springframework.beans.PropertyValue;
import org.springframework.beans.PropertyValues;
import org.springframework.dao.DataAccessException;
import org.springframework.dao.DataIntegrityViolationException;
import org.springframework.mock.web.MockHttpServletResponse;
import org.springframework.validation.BindException;
import org.springframework.validation.Errors;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.multipart.MultipartFile;
import org.springframework.web.servlet.ModelAndView;
import java.io.BufferedOutputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.nio.file.Path;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.TreeSet;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trimToEmpty;
import static org.labkey.api.action.ApiJsonWriter.CONTENT_TYPE_JSON;
import static org.labkey.api.assay.AssayFileWriter.ensureUploadDirectory;
import static org.labkey.api.data.DbScope.NO_OP_TRANSACTION;
import static org.labkey.api.query.AbstractQueryUpdateService.saveFile;
import static org.labkey.api.util.DOM.BR;
import static org.labkey.api.util.DOM.DIV;
import static org.labkey.api.util.DOM.FONT;
import static org.labkey.api.util.DOM.Renderable;
import static org.labkey.api.util.DOM.TABLE;
import static org.labkey.api.util.DOM.TD;
import static org.labkey.api.util.DOM.TR;
import static org.labkey.api.util.DOM.at;
import static org.labkey.api.util.DOM.cl;
import static org.labkey.query.MetadataTableJSON.getTableType;
import static org.labkey.query.MetadataTableJSON.parseDocument;
@SuppressWarnings("DefaultAnnotationParam")
public class QueryController extends SpringActionController
{
private static final Logger LOG = LogManager.getLogger(QueryController.class);
private static final String ROW_ATTACHMENT_INDEX_DELIM = "::";
private static final Set<String> RESERVED_VIEW_NAMES = CaseInsensitiveHashSet.of(
"Default",
AutoGeneratedDetailsCustomView.NAME,
AutoGeneratedInsertCustomView.NAME,
AutoGeneratedUpdateCustomView.NAME
);
private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(QueryController.class,
ValidateQueryAction.class,
ValidateQueriesAction.class,
GetSchemaQueryTreeAction.class,
GetQueryDetailsAction.class,
ViewQuerySourceAction.class
);
public QueryController()
{
setActionResolver(_actionResolver);
}
public static void registerAdminConsoleLinks()
{
AdminConsole.addLink(AdminConsole.SettingsLinkType.Diagnostics, "data sources", new ActionURL(DataSourceAdminAction.class, ContainerManager.getRoot()));
}
public static class RemoteQueryConnectionUrls
{
public static ActionURL urlManageRemoteConnection(Container c)
{
return new ActionURL(ManageRemoteConnectionsAction.class, c);
}
public static ActionURL urlCreateRemoteConnection(Container c)
{
return new ActionURL(EditRemoteConnectionAction.class, c);
}
public static ActionURL urlEditRemoteConnection(Container c, String connectionName)
{
ActionURL url = new ActionURL(EditRemoteConnectionAction.class, c);
url.addParameter("connectionName", connectionName);
return url;
}
public static ActionURL urlSaveRemoteConnection(Container c)
{
return new ActionURL(EditRemoteConnectionAction.class, c);
}
public static ActionURL urlDeleteRemoteConnection(Container c, @Nullable String connectionName)
{
ActionURL url = new ActionURL(DeleteRemoteConnectionAction.class, c);
if (connectionName != null)
url.addParameter("connectionName", connectionName);
return url;
}
public static ActionURL urlTestRemoteConnection(Container c, String connectionName)
{
ActionURL url = new ActionURL(TestRemoteConnectionAction.class, c);
url.addParameter("connectionName", connectionName);
return url;
}
}
@RequiresPermission(AdminOperationsPermission.class)
public static class EditRemoteConnectionAction extends FormViewAction<RemoteConnections.RemoteConnectionForm>
{
@Override
public void validateCommand(RemoteConnections.RemoteConnectionForm target, Errors errors)
{
}
@Override
public ModelAndView getView(RemoteConnections.RemoteConnectionForm remoteConnectionForm, boolean reshow, BindException errors)
{
remoteConnectionForm.setConnectionKind(RemoteConnections.CONNECTION_KIND_QUERY);
if (!errors.hasErrors())
{
String name = remoteConnectionForm.getConnectionName();
// package the remote-connection properties into the remoteConnectionForm and pass them along
Map<String, String> map1 = RemoteConnections.getRemoteConnection(RemoteConnections.REMOTE_QUERY_CONNECTIONS_CATEGORY, name, getContainer());
remoteConnectionForm.setUrl(map1.get("URL"));
remoteConnectionForm.setUserEmail(map1.get("user"));
remoteConnectionForm.setPassword(map1.get("password"));
remoteConnectionForm.setFolderPath(map1.get("container"));
}
setHelpTopic("remoteConnection");
return new JspView<>("/org/labkey/query/view/createRemoteConnection.jsp", remoteConnectionForm, errors);
}
@Override
public boolean handlePost(RemoteConnections.RemoteConnectionForm remoteConnectionForm, BindException errors)
{
return RemoteConnections.createOrEditRemoteConnection(remoteConnectionForm, getContainer(), errors);
}
@Override
public URLHelper getSuccessURL(RemoteConnections.RemoteConnectionForm remoteConnectionForm)
{
return RemoteQueryConnectionUrls.urlManageRemoteConnection(getContainer());
}
@Override
public void addNavTrail(NavTree root)
{
new BeginAction(getViewContext()).addNavTrail(root);
root.addChild("Create/Edit Remote Connection", new QueryUrlsImpl().urlExternalSchemaAdmin(getContainer()));
}
}
@RequiresPermission(AdminOperationsPermission.class)
public static class DeleteRemoteConnectionAction extends FormViewAction<RemoteConnections.RemoteConnectionForm>
{
@Override
public void validateCommand(RemoteConnections.RemoteConnectionForm target, Errors errors)
{
}
@Override
public ModelAndView getView(RemoteConnections.RemoteConnectionForm remoteConnectionForm, boolean reshow, BindException errors)
{
return new JspView<>("/org/labkey/query/view/confirmDeleteConnection.jsp", remoteConnectionForm, errors);
}
@Override
public boolean handlePost(RemoteConnections.RemoteConnectionForm remoteConnectionForm, BindException errors)
{
remoteConnectionForm.setConnectionKind(RemoteConnections.CONNECTION_KIND_QUERY);
return RemoteConnections.deleteRemoteConnection(remoteConnectionForm, getContainer());
}
@Override
public URLHelper getSuccessURL(RemoteConnections.RemoteConnectionForm remoteConnectionForm)
{
return RemoteQueryConnectionUrls.urlManageRemoteConnection(getContainer());
}
@Override
public void addNavTrail(NavTree root)
{
new BeginAction(getViewContext()).addNavTrail(root);
root.addChild("Confirm Delete Connection", new QueryUrlsImpl().urlExternalSchemaAdmin(getContainer()));
}
}
@RequiresPermission(AdminOperationsPermission.class)
public static class TestRemoteConnectionAction extends FormViewAction<RemoteConnections.RemoteConnectionForm>
{
@Override
public void validateCommand(RemoteConnections.RemoteConnectionForm target, Errors errors)
{
}
@Override
public ModelAndView getView(RemoteConnections.RemoteConnectionForm remoteConnectionForm, boolean reshow, BindException errors)
{
String name = remoteConnectionForm.getConnectionName();
String schemaName = "core"; // test Schema Name
String queryName = "Users"; // test Query Name
// Extract the username, password, and container from the secure property store
Map<String, String> singleConnectionMap = RemoteConnections.getRemoteConnection(RemoteConnections.REMOTE_QUERY_CONNECTIONS_CATEGORY, name, getContainer());
if (singleConnectionMap.isEmpty())
throw new NotFoundException();
String url = singleConnectionMap.get(RemoteConnections.FIELD_URL);
String user = singleConnectionMap.get(RemoteConnections.FIELD_USER);
String password = singleConnectionMap.get(RemoteConnections.FIELD_PASSWORD);
String container = singleConnectionMap.get(RemoteConnections.FIELD_CONTAINER);
// connect to the remote server and retrieve an input stream
org.labkey.remoteapi.Connection cn = new org.labkey.remoteapi.Connection(url, user, password);
final SelectRowsCommand cmd = new SelectRowsCommand(schemaName, queryName);
try
{
DataIteratorBuilder source = SelectRowsStreamHack.go(cn, container, cmd, getContainer());
// immediately close the source after opening it, this is a test.
source.getDataIterator(new DataIteratorContext()).close();
}
catch (Exception e)
{
errors.addError(new LabKeyError("The listed credentials for this remote connection failed to connect."));
return new JspView<>("/org/labkey/query/view/testRemoteConnectionsFailure.jsp", remoteConnectionForm);
}
return new JspView<>("/org/labkey/query/view/testRemoteConnectionsSuccess.jsp", remoteConnectionForm);
}
@Override
public boolean handlePost(RemoteConnections.RemoteConnectionForm remoteConnectionForm, BindException errors)
{
return true;
}
@Override
public URLHelper getSuccessURL(RemoteConnections.RemoteConnectionForm remoteConnectionForm)
{
return null;
}
@Override
public void addNavTrail(NavTree root)
{
new BeginAction(getViewContext()).addNavTrail(root);
root.addChild("Manage Remote Connections", new QueryUrlsImpl().urlExternalSchemaAdmin(getContainer()));
}
}
public static class QueryUrlsImpl implements QueryUrls
{
@Override
public ActionURL urlSchemaBrowser(Container c)
{
return new ActionURL(BeginAction.class, c);
}
@Override
public ActionURL urlSchemaBrowser(Container c, @Nullable String schemaName)
{
ActionURL ret = urlSchemaBrowser(c);
if (schemaName != null)
{
ret.addParameter(QueryParam.schemaName.toString(), schemaName);
}
return ret;
}
@Override
public ActionURL urlSchemaBrowser(Container c, @Nullable String schemaName, @Nullable String queryName)
{
if (StringUtils.isEmpty(queryName))
return urlSchemaBrowser(c, schemaName);
ActionURL ret = urlSchemaBrowser(c);
ret.addParameter(QueryParam.schemaName.toString(), trimToEmpty(schemaName));
ret.addParameter(QueryParam.queryName.toString(), trimToEmpty(queryName));
return ret;
}
public ActionURL urlExternalSchemaAdmin(Container c)
{
return urlExternalSchemaAdmin(c, null);
}
public ActionURL urlExternalSchemaAdmin(Container c, @Nullable String message)
{
ActionURL url = new ActionURL(AdminAction.class, c);
if (null != message)
url.addParameter("message", message);
return url;
}
public ActionURL urlInsertExternalSchema(Container c)
{
return new ActionURL(InsertExternalSchemaAction.class, c);
}
public ActionURL urlNewQuery(Container c)
{
return new ActionURL(NewQueryAction.class, c);
}
public ActionURL urlUpdateExternalSchema(Container c, AbstractExternalSchemaDef def)
{
ActionURL url = new ActionURL(EditExternalSchemaAction.class, c);
url.addParameter("externalSchemaId", Integer.toString(def.getExternalSchemaId()));
return url;
}
public ActionURL urlReloadExternalSchema(Container c, AbstractExternalSchemaDef def)
{
ActionURL url = new ActionURL(ReloadExternalSchemaAction.class, c);
url.addParameter("externalSchemaId", Integer.toString(def.getExternalSchemaId()));
return url;
}
public ActionURL urlDeleteSchema(Container c, AbstractExternalSchemaDef def)
{
ActionURL url = new ActionURL(DeleteSchemaAction.class, c);
url.addParameter("externalSchemaId", Integer.toString(def.getExternalSchemaId()));
return url;
}
@Override
public ActionURL urlStartBackgroundRReport(@NotNull ActionURL baseURL, String reportId)
{
ActionURL result = baseURL.clone();
result.setAction(ReportsController.StartBackgroundRReportAction.class);
result.replaceParameter(ReportDescriptor.Prop.reportId, reportId);
return result;
}
@Override
public ActionURL urlExecuteQuery(@NotNull ActionURL baseURL)
{
ActionURL result = baseURL.clone();
result.setAction(ExecuteQueryAction.class);
return result;
}
@Override
public ActionURL urlExecuteQuery(Container c, String schemaName, String queryName)
{
return new ActionURL(ExecuteQueryAction.class, c)
.addParameter(QueryParam.schemaName, schemaName)
.addParameter(QueryParam.queryName, queryName);
}
@Override
public @NotNull ActionURL urlCreateExcelTemplate(Container c, String schemaName, String queryName)
{
return new ActionURL(ExportExcelTemplateAction.class, c)
.addParameter(QueryParam.schemaName, schemaName)
.addParameter("query.queryName", queryName);
}
@Override
public ActionURL urlMetadataQuery(Container c, String schemaName, String queryName)
{
return new ActionURL(MetadataQueryAction.class, c)
.addParameter(QueryParam.schemaName, schemaName)
.addParameter(QueryParam.queryName, queryName);
}
}
@Override
public PageConfig defaultPageConfig()
{
// set default help topic for query controller
PageConfig config = super.defaultPageConfig();
config.setHelpTopic("querySchemaBrowser");
return config;
}
@AdminConsoleAction(AdminOperationsPermission.class)
public static class DataSourceAdminAction extends SimpleViewAction<Object>
{
public DataSourceAdminAction()
{
}
public DataSourceAdminAction(ViewContext viewContext)
{
setViewContext(viewContext);
}
@Override
public ModelAndView getView(Object o, BindException errors)
{
// Site Admin or Troubleshooter? Troubleshooters can see all the information but can't test data sources.
boolean hasAdminOpsPerms = getContainer().hasPermission(getUser(), AdminOperationsPermission.class);
List<ExternalSchemaDef> allDefs = QueryManager.get().getExternalSchemaDefs(null);
MultiValuedMap<String, ExternalSchemaDef> byDataSourceName = new ArrayListValuedHashMap<>();
for (ExternalSchemaDef def : allDefs)
byDataSourceName.put(def.getDataSource(), def);
MutableInt row = new MutableInt();
Renderable r = DOM.DIV(
DIV("This page lists all the data sources defined in your " + AppProps.getInstance().getWebappConfigurationFilename() + " file that were available when first referenced and the external schemas defined in each."),
BR(),
TABLE(cl("labkey-data-region"),
TR(cl("labkey-show-borders"),
hasAdminOpsPerms ? TD(cl("labkey-column-header"), "Test") : null,
TD(cl("labkey-column-header"), "Data Source"),
TD(cl("labkey-column-header"), "Current Status"),
TD(cl("labkey-column-header"), "URL"),
TD(cl("labkey-column-header"), "Database Name"),
TD(cl("labkey-column-header"), "Product Name"),
TD(cl("labkey-column-header"), "Product Version"),
TD(cl("labkey-column-header"), "Max Connections"),
TD(cl("labkey-column-header"), "Active Connections"),
TD(cl("labkey-column-header"), "Idle Connections"),
TD(cl("labkey-column-header"), "Max Wait (ms)")
),
DbScope.getDbScopes().stream()
.flatMap(scope -> {
String rowStyle = row.getAndIncrement() % 2 == 0 ? "labkey-alternate-row labkey-show-borders" : "labkey-row labkey-show-borders";
Object status;
boolean connected = false;
try (Connection ignore = scope.getConnection())
{
status = "connected";
connected = true;
}
catch (Exception e)
{
status = FONT(cl("labkey-error"), "disconnected");
}
return Stream.of(
TR(
cl(rowStyle),
hasAdminOpsPerms ? TD(connected ? new ButtonBuilder("Test").href(new ActionURL(TestDataSourceConfirmAction.class, getContainer()).addParameter("dataSource", scope.getDataSourceName())) : "") : null,
TD(HtmlString.NBSP, scope.getDisplayName()),
TD(status),
TD(scope.getDatabaseUrl()),
TD(scope.getDatabaseName()),
TD(scope.getDatabaseProductName()),
TD(scope.getDatabaseProductVersion()),
TD(scope.getDataSourceProperties().getMaxTotal()),
TD(scope.getDataSourceProperties().getNumActive()),
TD(scope.getDataSourceProperties().getNumIdle()),
TD(scope.getDataSourceProperties().getMaxWaitMillis())
),
TR(
cl(rowStyle),
TD(HtmlString.NBSP),
TD(at(DOM.Attribute.colspan, 10), getDataSourceTable(byDataSourceName.get(scope.getDataSourceName())))
)
);
})
)
);
return new HtmlView(r);
}
private Renderable getDataSourceTable(Collection<ExternalSchemaDef> dsDefs)
{
if (dsDefs.isEmpty())
return TABLE(TR(TD(HtmlString.NBSP)));
MultiValuedMap<String, ExternalSchemaDef> byContainerPath = new ArrayListValuedHashMap<>();
for (ExternalSchemaDef def : dsDefs)
byContainerPath.put(def.getContainerPath(), def);
TreeSet<String> paths = new TreeSet<>(byContainerPath.keySet());
return TABLE(paths.stream()
.map(path -> TR(TD(at(DOM.Attribute.colspan, 4), getDataSourcePath(path, byContainerPath.get(path)))))
);
}
private Renderable getDataSourcePath(String path, Collection<ExternalSchemaDef> unsorted)
{
List<ExternalSchemaDef> defs = new ArrayList<>(unsorted);
defs.sort(Comparator.comparing(AbstractExternalSchemaDef::getUserSchemaName, String.CASE_INSENSITIVE_ORDER));
Container c = ContainerManager.getForPath(path);
if (null == c)
return TD();
boolean hasRead = c.hasPermission(getUser(), ReadPermission.class);
QueryUrlsImpl urls = new QueryUrlsImpl();
return
TD(TABLE(
TR(TD(
at(DOM.Attribute.colspan, 3),
hasRead ? LinkBuilder.simpleLink(path, urls.urlExternalSchemaAdmin(c)) : path
)),
TR(TD(TABLE(
defs.stream()
.map(def -> TR(TD(
at(DOM.Attribute.style, "padding-left:20px"),
hasRead ? LinkBuilder.simpleLink(def.getUserSchemaName() +
(!Strings.CS.equals(def.getSourceSchemaName(), def.getUserSchemaName()) ? " (" + def.getSourceSchemaName() + ")" : ""), urls.urlUpdateExternalSchema(c, def))
: def.getUserSchemaName()
)))
)))
));
}
@Override
public void addNavTrail(NavTree root)
{
urlProvider(AdminUrls.class).addAdminNavTrail(root, "Data Source Administration", getClass(), getContainer());
}
}
public static class TestDataSourceForm
{
private String _dataSource;
public String getDataSource()
{
return _dataSource;
}
@SuppressWarnings("unused")
public void setDataSource(String dataSource)
{
_dataSource = dataSource;
}
}
public static class TestDataSourceConfirmForm extends TestDataSourceForm
{
private String _excludeSchemas;
private String _excludeTables;
public String getExcludeSchemas()
{
return _excludeSchemas;
}
@SuppressWarnings("unused")
public void setExcludeSchemas(String excludeSchemas)
{
_excludeSchemas = excludeSchemas;
}
public String getExcludeTables()
{
return _excludeTables;
}
@SuppressWarnings("unused")
public void setExcludeTables(String excludeTables)
{
_excludeTables = excludeTables;
}
}
@RequiresPermission(AdminOperationsPermission.class)
public static class TestDataSourceConfirmAction extends FormViewAction<TestDataSourceConfirmForm>
{
private DbScope _scope;
@Override
public ModelAndView getView(TestDataSourceConfirmForm form, boolean reshow, BindException errors) throws Exception
{
validateCommand(form, errors);
return new JspView<>("/org/labkey/query/view/testDataSourceConfirm.jsp", _scope);
}
@Override
public void validateCommand(TestDataSourceConfirmForm form, Errors errors)
{
_scope = DbScope.getDbScope(form.getDataSource());
if (null == _scope)
throw new NotFoundException("Could not resolve data source " + form.getDataSource());
}
@Override
public boolean handlePost(TestDataSourceConfirmForm form, BindException errors) throws Exception
{
saveTestDataSourceProperties(form);
return true;
}
@Override
public URLHelper getSuccessURL(TestDataSourceConfirmForm form)
{
return new ActionURL(TestDataSourceAction.class, getContainer()).addParameter("dataSource", _scope.getDataSourceName());
}
@Override
public void addNavTrail(NavTree root)
{
new DataSourceAdminAction(getViewContext()).addNavTrail(root);
root.addChild("Prepare Test of " + _scope.getDataSourceName());
}
}
@RequiresPermission(AdminOperationsPermission.class)
public static class TestDataSourceAction extends SimpleViewAction<TestDataSourceForm>
{
private DbScope _scope;
@Override
public ModelAndView getView(TestDataSourceForm form, BindException errors)
{
_scope = DbScope.getDbScope(form.getDataSource());
if (null == _scope)
throw new NotFoundException("Could not resolve data source " + form.getDataSource());
return new JspView<>("/org/labkey/query/view/testDataSource.jsp", _scope);
}
@Override
public void addNavTrail(NavTree root)
{
new DataSourceAdminAction(getViewContext()).addNavTrail(root);
root.addChild("Test " + _scope.getDataSourceName());
}
}
@RequiresPermission(AdminOperationsPermission.class)
public static class ResetDataSourcePropertiesAction extends FormHandlerAction<TestDataSourceForm>
{
@Override
public void validateCommand(TestDataSourceForm target, Errors errors)
{
}
@Override
public boolean handlePost(TestDataSourceForm form, BindException errors) throws Exception
{
WritablePropertyMap map = PropertyManager.getWritableProperties(getCategory(form.getDataSource()), false);
if (map != null)
map.delete();
return true;
}
@Override
public URLHelper getSuccessURL(TestDataSourceForm form)
{
return new ActionURL(TestDataSourceConfirmAction.class, getContainer()).addParameter("dataSource", form.getDataSource()) ;
}
}
private static final String TEST_DATA_SOURCE_CATEGORY = "testDataSourceProperties";
private static final String TEST_DATA_SOURCE_SCHEMAS_PROPERTY = "excludeSchemas";
private static final String TEST_DATA_SOURCE_TABLES_PROPERTY = "excludeTables";
private static String getCategory(String dataSourceName)
{
return TEST_DATA_SOURCE_CATEGORY + "|" + dataSourceName;
}