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bug with entry from plain text #12211

Closed
luca-ferrigno opened this issue Nov 18, 2024 · 8 comments
Closed

bug with entry from plain text #12211

luca-ferrigno opened this issue Nov 18, 2024 · 8 comments

Comments

@luca-ferrigno
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JabRef 5.15--2024-07-10--1eb3493
Windows 11 10.0 amd64
Java 21.0.2

Steps to reproduce:

  1. click on "new entry from plain text"
  2. insert citation
  3. "0 entries were parsed from your query."

Paste your log details here.

Detail information: 
Not updating theme because it hasn't changed
Theme set to Theme{type=DEFAULT, name=''} with base css StyleSheet{jrt:/org.jabref/org/jabref/gui/Base.css}
No open database detected
Opening: 'C:\Users\lucaf\Scuola\Università\Articoli\biblio.bib'
Resource "" not found.
Resource "" not found.
Java vector incubator module is not readable. For optimal vector performance, pass '--add-modules jdk.incubator.vector' to enable Vector API.
Problem parsing XMP schema. Continuing with other schemas.
java.io.IOException: org.apache.xmpbox.xml.XmpParsingException: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfXmpImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.externalfiles.ExternalFilesContentImporter.importPDFContent(Unknown Source)
	at [email protected]/org.jabref.gui.externalfiles.ImportHandler$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.externalfiles.ImportHandler$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.util.UiTaskExecutor$1.call(Unknown Source)
	at [email protected]/javafx.concurrent.Task$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: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.manageArray(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.createProperty(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parse(Unknown Source)
	... 16 more

Deleted 1 entry(ies)
Importing file (Aspects of Mathematics 6) Prof. Dr. Gerd Faltings, Prof. Dr. Gisbert W_stholz (auth.) - Rational Points_ Seminar Bonn_Wuppertal 1983_84-Vieweg+Teubner Verlag (1992).pdf as unknown format
Problem parsing XMP schema. Continuing with other schemas.
java.io.IOException: org.apache.xmpbox.xml.XmpParsingException: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfXmpImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$0(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.doImport(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.lambda$importSingleFile$1(Unknown Source)
	at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.util.UiTaskExecutor$1.call(Unknown Source)
	at [email protected]/javafx.concurrent.Task$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: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.manageArray(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.createProperty(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
	at [email protected]/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: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilShared.hasMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfXmpImporter.isRecognizedFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$1(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.doImport(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.lambda$importSingleFile$1(Unknown Source)
	at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.util.UiTaskExecutor$1.call(Unknown Source)
	at [email protected]/javafx.concurrent.Task$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: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.manageArray(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.createProperty(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parse(Unknown Source)
	... 19 more

Supplied encoding could not be determined
java.nio.charset.UnmappableCharacterException: Input length = 1
	at java.base/java.nio.charset.CoderResult.throwException(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.implRead(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.lockedRead(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.read(Unknown Source)
	at java.base/java.io.InputStreamReader.read(Unknown Source)
	at java.base/java.io.BufferedReader.fill(Unknown Source)
	at java.base/java.io.BufferedReader.implReadLine(Unknown Source)
	at java.base/java.io.BufferedReader.readLine(Unknown Source)
	at java.base/java.io.BufferedReader.readLine(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.BibtexImporter.getSuppliedEncoding(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.BibtexImporter.getEncodingResult(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$0(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.doImport(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.lambda$importSingleFile$1(Unknown Source)
	at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.util.UiTaskExecutor$1.call(Unknown Source)
	at [email protected]/javafx.concurrent.Task$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)

Problem parsing XMP schema. Continuing with other schemas.
java.io.IOException: org.apache.xmpbox.xml.XmpParsingException: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfXmpImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$0(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.doImport(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.lambda$importSingleFile$1(Unknown Source)
	at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.util.UiTaskExecutor$1.call(Unknown Source)
	at [email protected]/javafx.concurrent.Task$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: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.manageArray(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.createProperty(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
	at [email protected]/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: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.jabref.logic.xmp.XmpUtilShared.parseXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.getXmpMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilReader.readXmp(Unknown Source)
	at [email protected]/org.jabref.logic.xmp.XmpUtilShared.hasMetadata(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.PdfXmpImporter.isRecognizedFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$1(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.doImport(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.lambda$importSingleFile$1(Unknown Source)
	at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.util.UiTaskExecutor$1.call(Unknown Source)
	at [email protected]/javafx.concurrent.Task$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: Invalid array type, expecting Seq and found Bag [prefix=dc; name=creator]
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.manageArray(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.createProperty(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseChildrenAsProperties(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parseDescriptionRoot(Unknown Source)
	at [email protected]/org.apache.xmpbox.xml.DomXmpParser.parse(Unknown Source)
	... 19 more

Supplied encoding could not be determined
java.nio.charset.UnmappableCharacterException: Input length = 1
	at java.base/java.nio.charset.CoderResult.throwException(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.implRead(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.lockedRead(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.read(Unknown Source)
	at java.base/java.io.InputStreamReader.read(Unknown Source)
	at java.base/java.io.BufferedReader.fill(Unknown Source)
	at java.base/java.io.BufferedReader.implReadLine(Unknown Source)
	at java.base/java.io.BufferedReader.readLine(Unknown Source)
	at java.base/java.io.BufferedReader.readLine(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.BibtexImporter.getSuppliedEncoding(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.BibtexImporter.getEncodingResult(Unknown Source)
	at [email protected]/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.lambda$importUnknownFormat$0(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.logic.importer.ImportFormatReader.importUnknownFormat(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.doImport(Unknown Source)
	at [email protected]/org.jabref.gui.importer.ImportCommand.lambda$importSingleFile$1(Unknown Source)
	at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at [email protected]/org.jabref.gui.util.UiTaskExecutor$1.call(Unknown Source)
	at [email protected]/javafx.concurrent.Task$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
Your text is being parsed...
0 entries were parsed from your query.
Your text is being parsed...
0 entries were parsed from your query.
Deleted 1 entry(ies)
Your text is being parsed...
0 entries were parsed from your query.
External changes are resolved successfully
Library saved
Your text is being parsed...
0 entries were parsed from your query.
Library saved
Your text is being parsed...
0 entries were parsed from your query.
Library saved
Your text is being parsed...
0 entries were parsed from your query.
Library saved
Your text is being parsed...
0 entries were parsed from your query.
Library saved
Issue on GitHub successfully reported.
@koppor
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koppor commented Nov 19, 2024

@luca-ferrigno Could you paste the reference here? I assume, you have activated Grobid - and our Grobid server is probably down.

I tried with

O. Kopp, A. Armbruster, und O. Zimmermann, "Markdown Architectural Decision Records: Format and Tool Support", in 10th ZEUS Workshop, 2018.

Image

Result

@Book{Kopp2018,
  author    = {Kopp, A. and und, O. },
  publisher = { "Markdown Architectural Decision Records: Format and Tool Support"},
  title     = {Zimmermann},
  year      = {2018},
  comment   = {O. [author_tag]Armbruster, [author_tag]Zimmermann, "Markdown Architectural Decision Records: Format and Tool Support", in[pages_tag]th ZEUS Workshop, [year_tag].},
  pages     = { 10},
}

(Wrong entry type etc)

With LLM:

Image

@InProceedings{Kopp2018b,
  author    = {O. Kopp and A. Armbruster and O. Zimmermann},
  booktitle = {10th ZEUS Workshop},
  title     = {Markdown Architectural Decision Records: Format and Tool Support},
  year      = {2018},
}

@koppor
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koppor commented Mar 3, 2025

Did not hear any update. Maybe it is related to #10082

@koppor koppor closed this as not planned Won't fix, can't repro, duplicate, stale Mar 3, 2025
@ThiloteE
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ThiloteE commented Mar 3, 2025

I wrote new documentation for "entry from plain text". See https://docs.jabref.org/collect/newentryfromplaintext. I recommend trying the 6.0alpha release. Grobid is currently down, but LLM works.

@luca-ferrigno
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luca-ferrigno commented Mar 3, 2025 •
edited
Loading

I cannot select the parser, as there is no selection menu (see image attached). I'm currently using version 5.15 on Windows.

Image

@ThiloteE
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ThiloteE commented Mar 3, 2025

Yes, it is a new feature only available in JabRef 6.0alpha.

@ThiloteE
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ThiloteE commented Mar 3, 2025 •
edited
Loading

You can download the alpha version from here: https://builds.jabref.org/tags/v6.0-alpha/, but make sure to create a backup of your library files.

@luca-ferrigno
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Thank you!

@koppor
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koppor commented Mar 12, 2025

Releases are best downloaded from the releases page. --> https://github.com/JabRef/jabref/releases

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@koppor @ThiloteE @luca-ferrigno