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Errors when importing and/or drag and droping certain PDFs. #9383

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Kramer84 opened this issue Nov 18, 2022 · 1 comment · Fixed by #9385
Closed
2 tasks done

Errors when importing and/or drag and droping certain PDFs. #9383

Kramer84 opened this issue Nov 18, 2022 · 1 comment · Fixed by #9385
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bug Confirmed bugs or reports that are very likely to be bugs external files import

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@Kramer84
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JabRef version

Latest development branch build (please note build date below)

Operating system

GNU / Linux

Details on version and operating system

Ubuntu 20.04.5 - GNOME 3.36.5 - JabRef 5.8

Checked with the latest development build

  • I made a backup of my libraries before testing the latest development version.
  • I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

I have just started using JabRef and wanted to import all my local PDFs to create a bibliography file, but I encounter errors when importing certain PDF's :

  1. This happened with a specific PDF file . You can download it from this google drive link
  2. The errors arise when importing through the File->Import dialogue, as well as when drag and dropping.
  3. If multiple files were drag and dropped along with this one, the whole import operation stops once JabRef encounters the error.
  4. The log file error is different between the approaches, you can see both in the appendix.

I have tested this with JR 5.7 as well as the latest 5.8, but the error persists. It seems to be a problem with the xml parsing.

Appendix

...

Log File When Drag And Dropping 
Problem parsing XMP schema. Continuing with other schemas.
java.io.IOException: org.apache.xmpbox.xml.XmpParsingException: Cannot find a definition for the namespace http://crossref.org/crossmark/1.0/
	at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
	at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
	at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
	at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfXmpImporter.importDatabase(Unknown Source)
	at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter.importDatabase(Unknown Source)
	at org.jabref@5.8.239/org.jabref.logic.externalfiles.ExternalFilesContentImporter.importPDFContent(Unknown Source)
	at org.jabref@5.8.239/org.jabref.gui.externalfiles.ImportHandler$1.call(Unknown Source)
	at org.jabref@5.8.239/org.jabref.gui.externalfiles.ImportHandler$1.call(Unknown Source)
	at org.jabref@5.8.239/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
	at org.jabref.merged.module@5.8.239/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.apache.xmpbox.xml.XmpParsingException: Cannot find a definition for the namespace http://crossref.org/crossmark/1.0/
	at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.checkPropertyDefinition(Unknown Source)
	at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
	at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
	at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parse(Unknown Source)
	... 16 more
Log File When Using Import Dialogue 
Importing in unknown format...
Problem parsing XMP schema. Continuing with other schemas.
java.io.IOException: org.apache.xmpbox.xml.XmpParsingException: Cannot find a definition for the namespace http://prismstandard.org/namespaces/basic/2.0/
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfXmpImporter.importDatabase(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter.importDatabase(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$0(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.importer.ImportAction.doImport(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.importer.ImportAction.lambda$automatedImport$2(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
    at org.jabref.merged.module@5.8.239/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.apache.xmpbox.xml.XmpParsingException: Cannot find a definition for the namespace http://prismstandard.org/namespaces/basic/2.0/
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.checkPropertyDefinition(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parse(Unknown Source)
    ... 19 more

Problem parsing XMP schema. Continuing with other schemas.
java.io.IOException: org.apache.xmpbox.xml.XmpParsingException: Cannot find a definition for the namespace http://crossref.org/crossmark/1.0/
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfXmpImporter.importDatabase(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter.importDatabase(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$0(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.importer.ImportAction.doImport(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.importer.ImportAction.lambda$automatedImport$2(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
    at org.jabref.merged.module@5.8.239/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.apache.xmpbox.xml.XmpParsingException: Cannot find a definition for the namespace http://crossref.org/crossmark/1.0/
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.checkPropertyDefinition(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parse(Unknown Source)
    ... 19 more

Error importing
java.lang.IllegalArgumentException: prefix cannot be "null" when creating a QName
    at java.xml/javax.xml.namespace.QName.<init>(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomHelper.getQName(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
    at org.jabref.merged.module@5.8.239/org.apache.xmpbox.xml.DomXmpParser.parse(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfXmpImporter.importDatabase(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter.importDatabase(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$0(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
    at org.jabref@5.8.239/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.importer.ImportAction.doImport(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.importer.ImportAction.lambda$automatedImport$2(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
    at org.jabref@5.8.239/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
    at org.jabref.merged.module@5.8.239/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)

Import canceled
@Siedlerchr Siedlerchr added import bug Confirmed bugs or reports that are very likely to be bugs external files labels Nov 18, 2022
Siedlerchr added a commit that referenced this issue Nov 18, 2022
@Siedlerchr
Do not break on Exception in XMP parser
06cf451 
Fixes #9383

Workaround for IllegalArgumentException
@Siedlerchr Siedlerchr mentioned this issue Nov 18, 2022
Merged
6 tasks
Siedlerchr added a commit that referenced this issue Nov 18, 2022
@Siedlerchr
Do not break on Exception in XMP parser (#9385)
66424d2 
* Do not break on Exception in XMP parser


Fixes #9383

Workaround for IllegalArgumentException

* changelog

* Update check-links.yaml

ignore link checker for CHANGELOG
@Siedlerchr
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Thanks for raising this issue! I added a workaround so that the exception does not prevent the importer.
A new build will be ready in roughly 30 minutes.

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Do not break on Exception in XMP parser JabRef/jabref
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@Siedlerchr @Kramer84