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Can't generate new subsidiary bib file from aux file #8513

@wujastyk

Description

@wujastyk

JabRef version

Latest development branch build (please note build date below)

Operating system

GNU / Linux

Details on version and operating system

JabRef 5.6--2022-02-15--b33ebfb Linux 5.13.0-28-generic amd64 Java 17.0.2 JavaFX 17.0.2-ea+3

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'm using BibLaTeX.

  1. Tools / New subsidiary ...
  2. When I "parse" the aux file I get this

image

Appendix

...

Log File
Fix SSL exceptions by accepting ALL certificates
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}
Index path for /home/dom/Dropbox/localtexmf/bibtex/bib/biblio4-utf8.bib is /home/dom/.local/share/JabRef/0.5a
invalid url
java.net.MalformedURLException: no protocol: :/home/dom/GoogleDrive@Ualberta/DataDrive02/ebooks/Buddhism/www.ahandfulofleaves.org/documents/How Buddhism Began_Gombrich.pdf:PDF
	at java.base/java.net.URL.<init>(Unknown Source)
	at java.base/java.net.URL.<init>(Unknown Source)
	at java.base/java.net.URL.<init>(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.importer.util.FileFieldParser.parse(Unknown Source)
	at org.jabref@5.6.44/org.jabref.model.entry.BibEntry.getFiles(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.addToIndex(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.LibraryTab$IndexUpdateListener.<init>(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.LibraryTab.<init>(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.JabRefFrame.addTab(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.JabRefFrame.addParserResult(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.JabRefGUI.openDatabases(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
	at org.jabref.merged.module@5.6.44/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)

invalid url
java.net.MalformedURLException: no protocol: :https\://www.jstor.org/stable/24008036:URL
	at java.base/java.net.URL.<init>(Unknown Source)
	at java.base/java.net.URL.<init>(Unknown Source)
	at java.base/java.net.URL.<init>(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.importer.util.FileFieldParser.parse(Unknown Source)
	at org.jabref@5.6.44/org.jabref.model.entry.BibEntry.getFiles(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.addToIndex(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.LibraryTab$IndexUpdateListener.<init>(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.LibraryTab.<init>(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.JabRefFrame.addTab(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.JabRefFrame.addParserResult(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.JabRefGUI.openDatabases(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
	at org.jabref.merged.module@5.6.44/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
	at org.jabref.merged.module@5.6.44/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
[...]
java.io.IOException: Unknown dir object c=')' cInt=41 peek=')' peekInt=41 at offset 9892175 (start offset: 9892175)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.BaseParser.parseDirObject(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.BaseParser.parseCOSDictionaryValue(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.BaseParser.parseCOSDictionaryNameValuePair(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.BaseParser.parseCOSDictionary(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.BaseParser.parseDirObject(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.COSParser.parseFileObject(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.COSParser.parseObjectDynamically(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.COSParser.parseObjectDynamically(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.COSParser.parseTrailerValuesDynamically(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.PDFParser.initialParse(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.PDFParser.parse(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.DocumentReader.readPdfContents(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.DocumentReader.readLinkedPdf(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.PdfIndexer.writeToIndex(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.PdfIndexer.addToIndex(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.lambda$addToIndex$4(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.call(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.call(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
	at org.jabref.merged.module@5.6.44/javafx.concurrent.Task$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)

[...]
Could not read pdf file /home/dom/Dropbox/Library/Colleagues Papers/Franco, Eli/2996  JIP A new era in Buddhist studies.pdf!
java.io.IOException: Error: End-of-File, expected line
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.BaseParser.readLine(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.COSParser.parseHeader(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.COSParser.parsePDFHeader(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdfparser.PDFParser.parse(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref.merged.module@5.6.44/org.apache.pdfbox.pdmodel.PDDocument.load(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.DocumentReader.readPdfContents(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.DocumentReader.readLinkedPdf(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.PdfIndexer.writeToIndex(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.PdfIndexer.addToIndex(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.lambda$addToIndex$4(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.call(Unknown Source)
	at org.jabref@5.6.44/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.call(Unknown Source)
	at org.jabref@5.6.44/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
	at org.jabref.merged.module@5.6.44/javafx.concurrent.Task$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)

[...]
Could not find /home/dom/GoogleDriveUofA/DataDrive02/ebooks/Indology/Bisschop and Cecil_Primary Sources and Asian Pasts_2020.pdf
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