Report duplicate and overlapping database indices (#6989)

labkey-adam · web-flow · commit 5d821674c396 · 2025-09-04T12:06:45.000-07:00
diff --git a/.gitattributes b/.gitattributes
@@ -253,7 +253,6 @@ api/src/org/labkey/api/assay/AssaySaveHandler.java -text
 api/src/org/labkey/api/assay/AssaySchema.java -text
 api/src/org/labkey/api/assay/AssayService.java -text
 api/src/org/labkey/api/assay/AssayTableMetadata.java -text
-api/src/org/labkey/api/assay/AssayUploadFileResolver.java -text
 api/src/org/labkey/api/assay/AssayUploadXarContext.java -text
 api/src/org/labkey/api/assay/AssayUrls.java -text
 api/src/org/labkey/api/assay/AssayView.java -text
@@ -618,7 +617,6 @@ api/src/org/labkey/api/exceptions/TableNotFoundException.java -text
 api/src/org/labkey/api/exp/AbstractParameter.java -text
 api/src/org/labkey/api/exp/api/AbstractExperimentDataHandler.java -text
 api/src/org/labkey/api/exp/api/AbstractProtocolInputCriteria.java -text
-api/src/org/labkey/api/exp/api/AssayDomainType.java -text
 api/src/org/labkey/api/exp/api/AssayJSONConverter.java -text
 api/src/org/labkey/api/exp/api/DataType.java -text
 api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java -text
diff --git a/api/src/org/labkey/api/action/ConfirmAction.java b/api/src/org/labkey/api/action/ConfirmAction.java
@@ -77,7 +77,7 @@ public final ModelAndView handleRequest() throws Exception
                     ModelAndView mv = getSuccessView(form);
                     if (null != mv)
                         return mv;
-                    throw new RedirectException(getSuccessURL(form));
+                    throw new RedirectException(getSuccessURL(form), false);
                 }
             }
             else
diff --git a/api/src/org/labkey/api/settings/LookAndFeelProperties.java b/api/src/org/labkey/api/settings/LookAndFeelProperties.java
@@ -277,7 +277,7 @@ public Boolean isDiscussionEnabledStored()
 
     public String getUnsubstitutedLogoHref()
     {
-        return lookupStringValue(logoHref, AppProps.getInstance().getHomePageUrl().replaceAll("^" + AppProps.getInstance().getContextPath(), "\\${contextPath}"));
+        return lookupStringValue(logoHref, AppProps.getInstance().getHomePageActionURL().getLocalURIString().replaceAll("^" + AppProps.getInstance().getContextPath(), "\\${contextPath}"));
     }
 
     public String getUnsubstitutedLogoHrefStored()
diff --git a/api/src/org/labkey/api/view/HttpView.java b/api/src/org/labkey/api/view/HttpView.java
@@ -594,13 +594,12 @@ protected void renderInternal(Object model, PrintWriter out) throws IOException
 
     public static HttpView<?> redirect(URLHelper url, boolean allowAbsoluteUrl)
     {
-        String redirectUrl = (!allowAbsoluteUrl || url.isLocalUri(getRootContext())) ? url.getLocalURIString() : url.getURIString();
-        throw new RedirectException(redirectUrl);
+        throw new RedirectException(url, allowAbsoluteUrl);
     }
 
     public static HttpView<?> redirect(ActionURL url)
     {
-        throw new RedirectException(url.getLocalURIString());
+        throw new RedirectException(url);
     }
 
     /**
diff --git a/api/src/org/labkey/api/view/PermanentRedirectException.java b/api/src/org/labkey/api/view/PermanentRedirectException.java
@@ -5,12 +5,12 @@
 
 import jakarta.servlet.http.HttpServletResponse;
 
-/** Use when we want search engines, browsers, etc to assume that the redirecting URL is defunct and the target URL should be used going forward */
+/** Use when we want search engines, browsers, etc. to assume that the redirecting URL is defunct and the target URL should be used going forward */
 public class PermanentRedirectException extends RedirectException
 {
     public PermanentRedirectException(@NotNull URLHelper url)
     {
-        super(url);
+        super(url, false);
     }
 
     @Override
diff --git a/api/src/org/labkey/api/view/RedirectException.java b/api/src/org/labkey/api/view/RedirectException.java
@@ -29,7 +29,18 @@ public class RedirectException extends RuntimeException implements SkipMothershi
 {
     private final String _url;
 
+    @Deprecated // Call the variant that takes allowAbsoluteUrl
     public RedirectException(@NotNull URLHelper url)
+    {
+        this(url, false);
+    }
+
+    public RedirectException(@NotNull URLHelper url, boolean allowAbsoluteUrl)
+    {
+        this(!allowAbsoluteUrl || url.isLocalUri(HttpView.getRootContext()) ? url.getLocalURIString() : url.getURIString());
+    }
+
+    public RedirectException(@NotNull ActionURL url)
     {
         this(url.getLocalURIString());
     }
diff --git a/core/src/org/labkey/core/login/termsOfUse.jsp b/core/src/org/labkey/core/login/termsOfUse.jsp
@@ -42,7 +42,7 @@
 
     // Redirect immediately if terms are blank or null
     if (HtmlString.isBlank(termsHtml))
-        throw new RedirectException(returnUrl);
+        throw new RedirectException(returnUrl, false);
 
     ActionURL formURL = urlFor(AgreeToTermsAction.class);
 %>
diff --git a/core/src/org/labkey/core/thumbnail/ThumbnailCache.java b/core/src/org/labkey/core/thumbnail/ThumbnailCache.java
@@ -54,7 +54,7 @@ public static CacheableWriter getThumbnailWriter(ThumbnailProvider provider, Ima
             URLHelper redirectURL = ThumbnailUtil.getStaticThumbnailURL(provider, imageType);
 
             if (null != redirectURL)
-                throw new RedirectException(redirectURL);
+                throw new RedirectException(redirectURL, false);
         }
 
         return dynamic;
diff --git a/core/src/org/labkey/core/webdav/DavController.java b/core/src/org/labkey/core/webdav/DavController.java
@@ -18,6 +18,12 @@
 
 package org.labkey.core.webdav;
 
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponseWrapper;
+import jakarta.servlet.http.HttpSession;
+import jakarta.servlet.http.Part;
 import org.apache.commons.beanutils.ConversionException;
 import org.apache.commons.collections4.IteratorUtils;
 import org.apache.commons.io.FileUtils;
@@ -72,7 +78,28 @@
 import org.labkey.api.settings.LookAndFeelProperties;
 import org.labkey.api.settings.OptionalFeatureService;
 import org.labkey.api.test.TestWhen;
-import org.labkey.api.util.*;
+import org.labkey.api.util.CSRFException;
+import org.labkey.api.util.CSRFUtil;
+import org.labkey.api.util.ConfigurationException;
+import org.labkey.api.util.DateUtil;
+import org.labkey.api.util.ErrorRenderer;
+import org.labkey.api.util.ExceptionUtil;
+import org.labkey.api.util.FileStream;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.GUID;
+import org.labkey.api.util.HeartBeat;
+import org.labkey.api.util.HttpUtil;
+import org.labkey.api.util.MemTracker;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.Pair;
+import org.labkey.api.util.Path;
+import org.labkey.api.util.ResponseHelper;
+import org.labkey.api.util.ShutdownListener;
+import org.labkey.api.util.StringUtilsLabKey;
+import org.labkey.api.util.URIUtil;
+import org.labkey.api.util.URLHelper;
+import org.labkey.api.util.UnexpectedException;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.DefaultModelAndView;
@@ -115,14 +142,7 @@
 import org.xml.sax.SAXException;
 import org.xml.sax.helpers.DefaultHandler;
 
-import jakarta.servlet.ServletException;
-import jakarta.servlet.http.HttpServletRequest;
-import jakarta.servlet.http.HttpServletResponse;
-import jakarta.servlet.http.HttpServletResponseWrapper;
-import jakarta.servlet.http.HttpSession;
-import jakarta.servlet.http.Part;
 import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.parsers.SAXParser;
 import javax.xml.parsers.SAXParserFactory;
@@ -194,8 +214,6 @@
 
 
 /**
- * User: matthewb
- * Date: Oct 3, 2007
  * Derived from Tomcat's WebdavServlet
  */
 public class DavController extends SpringActionController
@@ -873,7 +891,7 @@ public final WebdavStatus doMethod() throws DavException, IOException
                     throw x;
                 // NOTE: AppProps.getInstance().getSiteWelcomePageUrlString() is handled before we even get here.  See WebdavServlet.
                 if (c.isRoot())
-                    throw new RedirectException(AppProps.getInstance().getHomePageUrl());
+                    throw new RedirectException(AppProps.getInstance().getHomePageActionURL());
                 throw new RedirectException(c.getStartURL(getUser()));
             }
         }
diff --git a/devtools/src/org/labkey/devtools/DevtoolsContainerListener.java b/devtools/src/org/labkey/devtools/DevtoolsContainerListener.java
diff --git a/devtools/src/org/labkey/devtools/DevtoolsManager.java b/devtools/src/org/labkey/devtools/DevtoolsManager.java
diff --git a/devtools/src/org/labkey/devtools/DevtoolsModule.java b/devtools/src/org/labkey/devtools/DevtoolsModule.java
@@ -17,7 +17,6 @@
 package org.labkey.devtools;
 
 import org.jetbrains.annotations.NotNull;
-import org.labkey.api.data.ContainerManager;
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.module.CodeOnlyModule;
 import org.labkey.api.module.ModuleContext;
@@ -72,8 +71,6 @@ protected void init()
     @Override
     public void doStartup(ModuleContext moduleContext)
     {
-        // add a container listener so we'll know when our container is deleted:
-        ContainerManager.addContainerListener(new DevtoolsContainerListener());
     }
 
     @Override
diff --git a/devtools/src/org/labkey/devtools/ToolsController.java b/devtools/src/org/labkey/devtools/ToolsController.java
diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java

Original file line number	Diff line number	Diff line change
`@@ -77,7 +77,7 @@ public final ModelAndView handleRequest() throws Exception`
`77`	`77`	`ModelAndView mv = getSuccessView(form);`
`78`	`78`	`if (null != mv)`
`79`	`79`	`return mv;`
`80`		`- throw new RedirectException(getSuccessURL(form));`
	`80`	`+ throw new RedirectException(getSuccessURL(form), false);`
`81`	`81`	`}`
`82`	`82`	`}`
`83`	`83`	`else`
Original file line number	Diff line number	Diff line change
`@@ -277,7 +277,7 @@ public Boolean isDiscussionEnabledStored()`
`277`	`277`
`278`	`278`	`public String getUnsubstitutedLogoHref()`
`279`	`279`	`{`
`280`		`- return lookupStringValue(logoHref, AppProps.getInstance().getHomePageUrl().replaceAll("^" + AppProps.getInstance().getContextPath(), "\\${contextPath}"));`
	`280`	`+ return lookupStringValue(logoHref, AppProps.getInstance().getHomePageActionURL().getLocalURIString().replaceAll("^" + AppProps.getInstance().getContextPath(), "\\${contextPath}"));`
`281`	`281`	`}`
`282`	`282`
`283`	`283`	`public String getUnsubstitutedLogoHrefStored()`
Original file line number	Diff line number	Diff line change
`@@ -594,13 +594,12 @@ protected void renderInternal(Object model, PrintWriter out) throws IOException`
`594`	`594`
`595`	`595`	`public static HttpView<?> redirect(URLHelper url, boolean allowAbsoluteUrl)`
`596`	`596`	`{`
`597`		`- String redirectUrl = (!allowAbsoluteUrl \|\| url.isLocalUri(getRootContext())) ? url.getLocalURIString() : url.getURIString();`
`598`		`- throw new RedirectException(redirectUrl);`
	`597`	`+ throw new RedirectException(url, allowAbsoluteUrl);`
`599`	`598`	`}`
`600`	`599`
`601`	`600`	`public static HttpView<?> redirect(ActionURL url)`
`602`	`601`	`{`
`603`		`- throw new RedirectException(url.getLocalURIString());`
	`602`	`+ throw new RedirectException(url);`
`604`	`603`	`}`
`605`	`604`
`606`	`605`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -5,12 +5,12 @@`
`5`	`5`
`6`	`6`	`import jakarta.servlet.http.HttpServletResponse;`
`7`	`7`
`8`		`-/** Use when we want search engines, browsers, etc to assume that the redirecting URL is defunct and the target URL should be used going forward */`
	`8`	`+/** Use when we want search engines, browsers, etc. to assume that the redirecting URL is defunct and the target URL should be used going forward */`
`9`	`9`	`public class PermanentRedirectException extends RedirectException`
`10`	`10`	`{`
`11`	`11`	`public PermanentRedirectException(@NotNull URLHelper url)`
`12`	`12`	`{`
`13`		`- super(url);`
	`13`	`+ super(url, false);`
`14`	`14`	`}`
`15`	`15`
`16`	`16`	`@Override`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,18 @@ public class RedirectException extends RuntimeException implements SkipMothershi`
`29`	`29`	`{`
`30`	`30`	`private final String _url;`
`31`	`31`
	`32`	`+ @Deprecated // Call the variant that takes allowAbsoluteUrl`
`32`	`33`	`public RedirectException(@NotNull URLHelper url)`
	`34`	`+ {`
	`35`	`+ this(url, false);`
	`36`	`+ }`
	`37`	`+`
	`38`	`+ public RedirectException(@NotNull URLHelper url, boolean allowAbsoluteUrl)`
	`39`	`+ {`
	`40`	`+ this(!allowAbsoluteUrl \|\| url.isLocalUri(HttpView.getRootContext()) ? url.getLocalURIString() : url.getURIString());`
	`41`	`+ }`
	`42`	`+`
	`43`	`+ public RedirectException(@NotNull ActionURL url)`
`33`	`44`	`{`
`34`	`45`	`this(url.getLocalURIString());`
`35`	`46`	`}`
Original file line number	Diff line number	Diff line change
`@@ -54,7 +54,7 @@ public static CacheableWriter getThumbnailWriter(ThumbnailProvider provider, Ima`
`54`	`54`	`URLHelper redirectURL = ThumbnailUtil.getStaticThumbnailURL(provider, imageType);`
`55`	`55`
`56`	`56`	`if (null != redirectURL)`
`57`		`- throw new RedirectException(redirectURL);`
	`57`	`+ throw new RedirectException(redirectURL, false);`
`58`	`58`	`}`
`59`	`59`
`60`	`60`	`return dynamic;`