Merge 24.11 to 25.2

Author: labkey-teamcity

panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ProteomeXchangeService.java

@@ -24,8 +24,10 @@
 import org.apache.hc.core5.http.HttpEntity;
 import org.apache.hc.core5.http.ParseException;
 import org.apache.hc.core5.http.io.entity.EntityUtils;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.logging.LogHelper;
 
 import java.io.File;
 import java.io.IOException;
@@ -45,6 +47,8 @@ public class ProteomeXchangeService
 
     private enum METHOD {submitDataset, validateXML, requestID}
 
+    private static final Logger LOG = LogHelper.getLogger(ProteomeXchangeService.class, "Handles requests to the ProteomeXchange server");
+
     public static String validatePxXml(File pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException
     {
         return postPxXml(pxxmlFile, testDatabase, user, pass, METHOD.validateXML);
@@ -86,7 +90,7 @@ public static String getPxIdResponse(boolean testDatabase, String user, String p
         }
         catch (Exception e)
         {
-            throw new ProteomeXchangeServiceException("Error requesting a ID from ProteomeXchange.", e);
+            throw new ProteomeXchangeServiceException("Error requesting a ID from ProteomeXchange. " + e.getMessage(), e);
         }
 
         return responseMessage;
@@ -160,6 +164,7 @@ private static String postRequest(MultipartEntityBuilder builder) throws IOExcep
                 int statusCode = response.getCode();
                 if (statusCode != 200)
                 {
+                    LOG.error("Unsuccessful request to ProteomeXchange.  Status code: " + statusCode + "; Response: " + responseMessage);
                     throw new ProteomeXchangeServiceException("Error " + statusCode + " from ProteomeXchange server: " + responseMessage);
                 }
                 return responseMessage;

panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ProteomeXchangeServiceException.java

@@ -15,7 +15,9 @@
  */
 package org.labkey.panoramapublic.proteomexchange;
 
-public class ProteomeXchangeServiceException extends Exception
+import org.labkey.api.util.SkipMothershipLogging;
+
+public class ProteomeXchangeServiceException extends Exception implements SkipMothershipLogging
 {
     public ProteomeXchangeServiceException(String message, Throwable cause)
     {

panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxXmlWriter.java

@@ -391,7 +391,7 @@ void writeModificationList(Status validationStatus) throws PxException
          */
         Element mod_list = new Element("ModificationList");
         var mods = validationStatus.getModifications();
-        if(mods.size() == 0)
+        if(mods.size() == 0 || mods.stream().noneMatch(Modification::isValid))
         {
             mod_list.addChild(new CvParamElement("MS", "MS:1002864", "No PTMs are included in the dataset"));
         }