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Merge pull request #11827 from QualitativeDataRepository/Payara-6.2025.9
Payara 6.2025.10 update
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The recommended Payara version has been updated to Payara-6.2025.10
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Payara 6.2025.10 cannot be used with earlier versions of Dataverse, e.g. v6.8.
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Standard Payara upgrade instructions - as in the 6.7 release notes should be added,
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but we should assure the instructions don't have you trying to run 6.8 with the latest Payara
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and perhaps should explicitly note that you can't.
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We should also change the 'standard' language related to Payara updates to include copying the
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*.p12 files from the distributed domain1/config directory into the Dataverse domain1/config directory,
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at least if/when they are different. Those files include base certs and over time using the old files
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can cause SSL errors. If the domain.xml file is old enough, it may also reference *.jks files instead
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of the *.p12 ones. That should also be fixed (domain.xml having those lines updated to reference *.p12 files).
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FWIW: I ran across this at TDL where a dev machine stopped being able to contact DataCite because the root
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cert used by DataCite today is not in the *.jks files that had been copied forward during Payara updates.)
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doc/sphinx-guides/source/developers/classic-dev-env.rst

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Install Payara
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~~~~~~~~~~~~~~
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Payara 6.2025.3 or higher is required.
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Payara 6.2025.10 or higher is required.
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To install Payara, run the following commands:
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``cd /usr/local``
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``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.3/payara-6.2025.3.zip``
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``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.10/payara-6.2025.10.zip``
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``sudo unzip payara-6.2025.3.zip``
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``sudo unzip payara-6.2025.10.zip``
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``sudo chown -R $USER /usr/local/payara6``
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doc/sphinx-guides/source/installation/prerequisites.rst

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Payara
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------
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Payara 6.2025.3 is recommended. Newer versions might work fine. Regular updates are recommended.
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Payara 6.2025.10 is recommended. Newer versions might work fine. Regular updates are recommended.
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Installing Payara
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=================
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- Download and install Payara (installed in ``/usr/local/payara6`` in the example commands below)::
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# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.3/payara-6.2025.3.zip
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# unzip payara-6.2025.3.zip
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# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2025.10/payara-6.2025.10.zip
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# unzip payara-6.2025.10.zip
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# mv payara6 /usr/local
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If nexus.payara.fish is ever down for maintenance, Payara distributions are also available from https://repo1.maven.org/maven2/fish/payara/distributions/payara/

doc/sphinx-guides/source/qa/test-automation.md

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```
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TASK [dataverse : download payara zip] *****************************************
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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"}
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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"}
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```
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In the example above, if Payara can't be downloaded, we're obviously going to have problems deploying Dataverse to it!

modules/dataverse-parent/pom.xml

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<argLine>-Duser.timezone=${project.timezone} -Dfile.encoding=${project.build.sourceEncoding} -Duser.language=${project.language} -Duser.region=${project.region}</argLine>
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<!-- Major system components and dependencies -->
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<payara.version>6.2025.3</payara.version>
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<payara.version>6.2025.10</payara.version>
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<postgresql.version>42.7.7</postgresql.version>
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<solr.version>9.8.0</solr.version>
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<aws.version>2.33.0</aws.version>

pom.xml

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<includes>
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<include>*.properties</include>
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<include>**/*.properties</include>
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<!-- As of https://github.com/payara/Payara/issues/7741, Payara uses the jakarta.mime.types file.
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The original mime.types file (with the same content) is retained to support the FileUtilTest.testGZipFile.
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-->
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<include>**/jakarta.mime.types</include>
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<include>**/mime.types</include>
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<include>**/*.R</include>
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</includes>
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# Common document formats
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application/pdf pdf PDF
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application/msword doc DOC
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application/vnd.ms-excel xls XLS xlc XLC xll XLL xlm XLM xlw XLW
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application/vnd.openxmlformats-officedocument.spreadsheetml.sheet xlsx XLSX
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text/comma-separated-values csv CSV
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text/plain txt TXT
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text/xml xml XML
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# Common statistical data formats
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text/tsv tab TAB tsv TSV
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text/x-fixed-field dat DAT asc ASC
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application/x-rlang-transport Rdata RData rdata RDATA
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type/x-r-syntax r R
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application/x-stata dta DTA
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text/x-stata-syntax do DO
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application/x-spss-sav sav SAV
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application/x-spss-por por POR
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text/x-spss-syntax sps SPS
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application/x-sas-transport xpt XPT cport CPORT v5x V5X v6x V6X v7x V7X
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application/x-sas-system sas7bdat SAS7BDAT sd1 SD1 sd2 SD2 sd7 SD7 ssd01 SSD01 ssd SSD ssd04 SSD04
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text/x-sas-syntax sas SAS
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# Common image formats
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image/gif gif GIF
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image/jpeg jpeg JPEG jpg JPG jpe JPE
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image/bmp bmp BMP
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image/x-portable-bitmap pbm PBM
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image/x-portable-graymap pgm PGM
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image/png png PNG
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image/x-portable-anymap pnm PNM
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image/x-portable-pixmap ppm PPM
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image/cmu-raster ras RAS
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image/x-rgb rgb RGB
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image/tiff tif TIF tiff TIFF
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image/x-xbitmap xbm XBM
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image/x-xpixmap xpm XPM
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image/x-xwindowdump xwd XWD
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# Common archive formats
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application/zip zip ZIP
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application/x-gzip gz GZ
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application/x-tar tar TAR
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# Rdata
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application/octet-stream

src/main/java/META-INF/mime.types

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# Common document formats
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application/pdf pdf PDF
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application/msword doc DOC
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application/vnd.ms-excel xls XLS xlc XLC xll XLL xlm XLM xlw XLW
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application/vnd.openxmlformats-officedocument.spreadsheetml.sheet xlsx XLSX
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text/comma-separated-values csv CSV
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text/plain txt TXT
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text/xml xml XML
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# Common statistical data formats
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text/tsv tab TAB tsv TSV
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text/x-fixed-field dat DAT asc ASC
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application/x-rlang-transport Rdata RData rdata RDATA
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type/x-r-syntax r R
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application/x-stata dta DTA
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text/x-stata-syntax do DO
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application/x-spss-sav sav SAV
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application/x-spss-por por POR
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text/x-spss-syntax sps SPS
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application/x-sas-transport xpt XPT cport CPORT v5x V5X v6x V6X v7x V7X
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application/x-sas-system sas7bdat SAS7BDAT sd1 SD1 sd2 SD2 sd7 SD7 ssd01 SSD01 ssd SSD ssd04 SSD04
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text/x-sas-syntax sas SAS
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# Common image formats
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image/gif gif GIF
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image/jpeg jpeg JPEG jpg JPG jpe JPE
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image/bmp bmp BMP
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image/x-portable-bitmap pbm PBM
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image/x-portable-graymap pgm PGM
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image/png png PNG
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image/x-portable-anymap pnm PNM
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image/x-portable-pixmap ppm PPM
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image/cmu-raster ras RAS
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image/x-rgb rgb RGB
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image/tiff tif TIF tiff TIFF
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image/x-xbitmap xbm XBM
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image/x-xpixmap xpm XPM
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image/x-xwindowdump xwd XWD
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# Common archive formats
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application/zip zip ZIP
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application/x-gzip gz GZ
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application/x-tar tar TAR
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# Rdata
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# mime.types is a copy of jakarta.mime.types which only used in unit tests (specifically FileUtilTest.testGZipFile)
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# Common document formats
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application/pdf pdf PDF
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application/msword doc DOC
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application/vnd.ms-excel xls XLS xlc XLC xll XLL xlm XLM xlw XLW
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application/vnd.openxmlformats-officedocument.spreadsheetml.sheet xlsx XLSX
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text/comma-separated-values csv CSV
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text/plain txt TXT
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text/xml xml XML
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# Common statistical data formats
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text/tsv tab TAB tsv TSV
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text/x-fixed-field dat DAT asc ASC
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application/x-rlang-transport Rdata RData rdata RDATA
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type/x-r-syntax r R
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application/x-stata dta DTA
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text/x-stata-syntax do DO
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application/x-spss-sav sav SAV
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application/x-spss-por por POR
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text/x-spss-syntax sps SPS
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application/x-sas-transport xpt XPT cport CPORT v5x V5X v6x V6X v7x V7X
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application/x-sas-system sas7bdat SAS7BDAT sd1 SD1 sd2 SD2 sd7 SD7 ssd01 SSD01 ssd SSD ssd04 SSD04
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text/x-sas-syntax sas SAS
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# Common image formats
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image/gif gif GIF
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image/jpeg jpeg JPEG jpg JPG jpe JPE
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image/bmp bmp BMP
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image/x-portable-bitmap pbm PBM
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image/x-portable-graymap pgm PGM
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image/png png PNG
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image/x-portable-anymap pnm PNM
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image/x-portable-pixmap ppm PPM
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image/cmu-raster ras RAS
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image/x-rgb rgb RGB
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image/tiff tif TIF tiff TIFF
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image/x-xbitmap xbm XBM
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image/x-xpixmap xpm XPM
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image/x-xwindowdump xwd XWD
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# Common archive formats
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application/zip zip ZIP
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application/x-gzip gz GZ
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application/x-tar tar TAR
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# Rdata
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application/octet-stream

src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java

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*
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* @author skraffmiller
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*/
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@NamedStoredProcedureQuery(
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name = "GuestbookResponse.estimateGuestBookResponseTableSize",
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procedureName = "estimateGuestBookResponseTableSize",
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parameters = {
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@StoredProcedureParameter(mode = ParameterMode.OUT, type = Long.class)
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}
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)
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@Entity
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@Table(indexes = {
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@Index(columnList = "guestbook_id"),

src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java

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// somehow. -- L.A. 5.6
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try {
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StoredProcedureQuery query = this.em.createNamedStoredProcedureQuery("GuestbookResponse.estimateGuestBookResponseTableSize");
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query.execute();
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Long totalCount = (Long) query.getOutputParameterValue(1);
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if (totalCount != null) {
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return totalCount;
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}
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} catch (IllegalArgumentException iae) {
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// Don't do anything, we'll fall back to using "SELECT COUNT()"
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// In GuestbookResponseServiceBean.java
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try {
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Query query = em.createNativeQuery("SELECT estimateGuestBookResponseTableSize()");
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return ((Number) query.getSingleResult()).longValue();
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} catch (Exception e) {
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// Fall back to using "SELECT COUNT()"
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}
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Query query = em.createNativeQuery("select count(o.id) from GuestbookResponse o where eventtype != '" + GuestbookResponse.ACCESS_REQUEST +"';");
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return (Long) query.getSingleResult();

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