Merge pull request #11827 from QualitativeDataRepository/Payara-6.2025.9

landreev · web-flow · commit f2a250f52fbb · 2025-12-05T17:11:36.000-05:00
Payara 6.2025.10 update
diff --git a/doc/release-notes/11827-Payara-6.2025.10.md b/doc/release-notes/11827-Payara-6.2025.10.md
@@ -0,0 +1,16 @@
+The recommended Payara version has been updated to Payara-6.2025.10
+
+Payara 6.2025.10 cannot be used with earlier versions of Dataverse, e.g. v6.8.
+
+Standard Payara upgrade instructions - as in the 6.7 release notes should be added, 
+but we should assure the instructions don't have you trying to run 6.8 with the latest Payara 
+and perhaps should explicitly note that you can't. 
+
+We should also change the 'standard' language related to Payara updates to include copying the
+*.p12 files from the distributed domain1/config directory into the Dataverse domain1/config directory,
+at least if/when they are different. Those files include base certs and over time using the old files
+can cause SSL errors. If the domain.xml file is old enough, it may also reference *.jks files instead
+of the *.p12 ones. That should also be fixed (domain.xml having those lines updated to reference *.p12 files).
+FWIW: I ran across this at TDL where a dev machine stopped being able to contact DataCite because the root
+cert used by DataCite today is not in the *.jks files that had been copied forward during Payara updates.)
+
diff --git a/doc/sphinx-guides/source/developers/classic-dev-env.rst b/doc/sphinx-guides/source/developers/classic-dev-env.rst
@@ -93,15 +93,15 @@ On Linux, install ``jq`` from your package manager or download a binary from htt
 Install Payara
 ~~~~~~~~~~~~~~
 
-Payara 6.2025.3 or higher is required.
+Payara 6.2025.10 or higher is required.
 
 To install Payara, run the following commands:
 
 ``cd /usr/local``
 
-``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.3/payara-6.2025.3.zip``
+``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.10/payara-6.2025.10.zip``
 
-``sudo unzip payara-6.2025.3.zip``
+``sudo unzip payara-6.2025.10.zip``
 
 ``sudo chown -R $USER /usr/local/payara6``
 
diff --git a/doc/sphinx-guides/source/installation/prerequisites.rst b/doc/sphinx-guides/source/installation/prerequisites.rst
@@ -44,7 +44,7 @@ On RHEL/derivative you can make Java 17 the default with the ``alternatives`` co
 Payara
 ------
 
-Payara 6.2025.3 is recommended. Newer versions might work fine. Regular updates are recommended.
+Payara 6.2025.10 is recommended. Newer versions might work fine. Regular updates are recommended.
 
 Installing Payara
 =================
@@ -55,8 +55,8 @@ Installing Payara
 
 - Download and install Payara (installed in ``/usr/local/payara6`` in the example commands below)::
 
-	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.3/payara-6.2025.3.zip
-	# unzip payara-6.2025.3.zip
+	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.10/payara-6.2025.10.zip
+	# unzip payara-6.2025.10.zip
 	# mv payara6 /usr/local
 
 If nexus.payara.fish is ever down for maintenance, Payara distributions are also available from https://repo1.maven.org/maven2/fish/payara/distributions/payara/
diff --git a/doc/sphinx-guides/source/qa/test-automation.md b/doc/sphinx-guides/source/qa/test-automation.md
@@ -52,7 +52,7 @@ Go to the end of the log and then scroll up, looking for the failure. A failed A
 
 ```
 TASK [dataverse : download payara zip] *****************************************
-fatal: [localhost]: FAILED! => {"changed": false, "dest": "/tmp/payara.zip", "elapsed": 10, "msg": "Request failed: <urlopen error timed out>", "url": "https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.3/payara-6.2025.3.zip"}
+fatal: [localhost]: FAILED! => {"changed": false, "dest": "/tmp/payara.zip", "elapsed": 10, "msg": "Request failed: <urlopen error timed out>", "url": "https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.10/payara-6.2025.10.zip"}
 ```
 
 In the example above, if Payara can't be downloaded, we're obviously going to have problems deploying Dataverse to it!
diff --git a/modules/dataverse-parent/pom.xml b/modules/dataverse-parent/pom.xml
@@ -149,7 +149,7 @@
         <argLine>-Duser.timezone=${project.timezone} -Dfile.encoding=${project.build.sourceEncoding} -Duser.language=${project.language} -Duser.region=${project.region}</argLine>
     
         <!-- Major system components and dependencies -->
-        <payara.version>6.2025.3</payara.version>
+        <payara.version>6.2025.10</payara.version>
         <postgresql.version>42.7.7</postgresql.version>
         <solr.version>9.8.0</solr.version>
         <aws.version>2.33.0</aws.version>
diff --git a/pom.xml b/pom.xml
@@ -838,6 +838,10 @@
                 <includes>
                     <include>*.properties</include>
                     <include>**/*.properties</include>
+                    <!-- As of https://github.com/payara/Payara/issues/7741, Payara uses the jakarta.mime.types file. 
+                         The original mime.types file (with the same content) is retained to support the FileUtilTest.testGZipFile.
+                     -->
+                    <include>**/jakarta.mime.types</include>
                     <include>**/mime.types</include>
                     <include>**/*.R</include>
                 </includes>
diff --git a/src/main/java/META-INF/jakarta.mime.types b/src/main/java/META-INF/jakarta.mime.types
@@ -0,0 +1,42 @@
+# Common document formats
+application/pdf pdf PDF
+application/msword doc DOC
+application/vnd.ms-excel xls XLS xlc XLC xll XLL xlm XLM xlw XLW
+application/vnd.openxmlformats-officedocument.spreadsheetml.sheet xlsx XLSX
+text/comma-separated-values csv CSV
+text/plain txt TXT
+text/xml xml XML
+# Common statistical data formats
+text/tsv tab TAB tsv TSV
+text/x-fixed-field dat DAT asc ASC
+application/x-rlang-transport Rdata RData rdata RDATA
+type/x-r-syntax r R
+application/x-stata dta DTA
+text/x-stata-syntax do DO
+application/x-spss-sav sav SAV
+application/x-spss-por por POR
+text/x-spss-syntax sps SPS
+application/x-sas-transport xpt XPT cport CPORT v5x V5X v6x V6X v7x V7X
+application/x-sas-system sas7bdat SAS7BDAT sd1 SD1 sd2 SD2 sd7 SD7 ssd01 SSD01 ssd SSD ssd04 SSD04
+text/x-sas-syntax sas SAS
+# Common image formats
+image/gif gif GIF
+image/jpeg jpeg JPEG jpg JPG jpe JPE
+image/bmp bmp BMP
+image/x-portable-bitmap pbm PBM
+image/x-portable-graymap pgm PGM
+image/png png PNG
+image/x-portable-anymap pnm PNM
+image/x-portable-pixmap ppm PPM
+image/cmu-raster ras RAS
+image/x-rgb rgb RGB
+image/tiff tif TIF tiff TIFF
+image/x-xbitmap xbm XBM
+image/x-xpixmap xpm XPM
+image/x-xwindowdump xwd XWD
+# Common archive formats
+application/zip zip ZIP
+application/x-gzip gz GZ
+application/x-tar tar TAR
+# Rdata
+application/octet-stream
diff --git a/src/main/java/META-INF/mime.types b/src/main/java/META-INF/mime.types
@@ -1,42 +1,43 @@
-# Common document formats
-application/pdf pdf PDF
-application/msword doc DOC
-application/vnd.ms-excel xls XLS xlc XLC xll XLL xlm XLM xlw XLW
-application/vnd.openxmlformats-officedocument.spreadsheetml.sheet xlsx XLSX
-text/comma-separated-values csv CSV
-text/plain txt TXT
-text/xml xml XML
-# Common statistical data formats
-text/tsv tab TAB tsv TSV
-text/x-fixed-field dat DAT asc ASC
-application/x-rlang-transport Rdata RData rdata RDATA
-type/x-r-syntax r R
-application/x-stata dta DTA
-text/x-stata-syntax do DO
-application/x-spss-sav sav SAV
-application/x-spss-por por POR
-text/x-spss-syntax sps SPS
-application/x-sas-transport xpt XPT cport CPORT v5x V5X v6x V6X v7x V7X
-application/x-sas-system sas7bdat SAS7BDAT sd1 SD1 sd2 SD2 sd7 SD7 ssd01 SSD01 ssd SSD ssd04 SSD04
-text/x-sas-syntax sas SAS
-# Common image formats
-image/gif gif GIF
-image/jpeg jpeg JPEG jpg JPG jpe JPE
-image/bmp bmp BMP
-image/x-portable-bitmap pbm PBM
-image/x-portable-graymap pgm PGM
-image/png png PNG
-image/x-portable-anymap pnm PNM
-image/x-portable-pixmap ppm PPM
-image/cmu-raster ras RAS
-image/x-rgb rgb RGB
-image/tiff tif TIF tiff TIFF
-image/x-xbitmap xbm XBM
-image/x-xpixmap xpm XPM
-image/x-xwindowdump xwd XWD
-# Common archive formats
-application/zip zip ZIP
-application/x-gzip gz GZ
-application/x-tar tar TAR
-# Rdata
+# mime.types is a copy of jakarta.mime.types which only used in unit tests (specifically FileUtilTest.testGZipFile)
+# Common document formats
+application/pdf pdf PDF
+application/msword doc DOC
+application/vnd.ms-excel xls XLS xlc XLC xll XLL xlm XLM xlw XLW
+application/vnd.openxmlformats-officedocument.spreadsheetml.sheet xlsx XLSX
+text/comma-separated-values csv CSV
+text/plain txt TXT
+text/xml xml XML
+# Common statistical data formats
+text/tsv tab TAB tsv TSV
+text/x-fixed-field dat DAT asc ASC
+application/x-rlang-transport Rdata RData rdata RDATA
+type/x-r-syntax r R
+application/x-stata dta DTA
+text/x-stata-syntax do DO
+application/x-spss-sav sav SAV
+application/x-spss-por por POR
+text/x-spss-syntax sps SPS
+application/x-sas-transport xpt XPT cport CPORT v5x V5X v6x V6X v7x V7X
+application/x-sas-system sas7bdat SAS7BDAT sd1 SD1 sd2 SD2 sd7 SD7 ssd01 SSD01 ssd SSD ssd04 SSD04
+text/x-sas-syntax sas SAS
+# Common image formats
+image/gif gif GIF
+image/jpeg jpeg JPEG jpg JPG jpe JPE
+image/bmp bmp BMP
+image/x-portable-bitmap pbm PBM
+image/x-portable-graymap pgm PGM
+image/png png PNG
+image/x-portable-anymap pnm PNM
+image/x-portable-pixmap ppm PPM
+image/cmu-raster ras RAS
+image/x-rgb rgb RGB
+image/tiff tif TIF tiff TIFF
+image/x-xbitmap xbm XBM
+image/x-xpixmap xpm XPM
+image/x-xwindowdump xwd XWD
+# Common archive formats
+application/zip zip ZIP
+application/x-gzip gz GZ
+application/x-tar tar TAR
+# Rdata
 application/octet-stream
diff --git a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java
@@ -26,13 +26,6 @@
  *
  * @author skraffmiller
  */
-@NamedStoredProcedureQuery(
-        name = "GuestbookResponse.estimateGuestBookResponseTableSize",
-        procedureName = "estimateGuestBookResponseTableSize",
-        parameters = {
-            @StoredProcedureParameter(mode = ParameterMode.OUT, type = Long.class)
-        }
-)
 @Entity
 @Table(indexes = {
         @Index(columnList = "guestbook_id"),
diff --git a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java
@@ -951,16 +951,12 @@ public Long getTotalDownloadCount() {
         // somehow. -- L.A. 5.6
         
         
-        try {        
-            StoredProcedureQuery query = this.em.createNamedStoredProcedureQuery("GuestbookResponse.estimateGuestBookResponseTableSize");
-            query.execute();
-            Long totalCount = (Long) query.getOutputParameterValue(1);
-        
-            if (totalCount != null) {
-                return totalCount;
-            }
-        } catch (IllegalArgumentException iae) {
-            // Don't do anything, we'll fall back to using "SELECT COUNT()"
+     // In GuestbookResponseServiceBean.java
+        try {
+            Query query = em.createNativeQuery("SELECT estimateGuestBookResponseTableSize()");
+            return ((Number) query.getSingleResult()).longValue();
+        } catch (Exception e) {
+            // Fall back to using "SELECT COUNT()"
         }
         Query query = em.createNativeQuery("select count(o.id) from GuestbookResponse  o where eventtype != '" + GuestbookResponse.ACCESS_REQUEST +"';");
         return (Long) query.getSingleResult();
