5.11.0: export produces nothing though all sheets reach PAGE — RunTable.afterUnmarshal NPE, and the binary-restart fallback throws FileSystemAlreadyExistsException

[jdburrage]

Summary

A book in which every sheet transcribes successfully can still export nothing. During
Book.export, reloading a sheet's persisted structure throws
NullPointerException: Cannot read the array length because "this.sequences" is null from
RunTable.afterUnmarshal. The recovery path then fails too, because reopening the book's
zip filesystem throws FileSystemAlreadyExistsException. The null sheet finally surfaces
as an NPE in Voices.refineScore, and no MusicXML is produced.

Two separate defects are visible in the one trace, and I think the second is worth fixing
independently of the first: the fallback that exists to rescue this situation cannot work.

Environment

Audiveris 5.11.0, build 9e1e55cd2746037d059345881c53e6a6754bffbd
Windows 11 10.0, amd64
OpenJDK 64-Bit Server VM (build 25.0.3+9-LTS, mixed mode)
Tesseract OCR 5.5.2

Minimal reproducer

Haydn, Symphony No. 45 "Farewell", Timothy Lanfear 2020 engraving — freely downloadable
from IMSLP as file #633504:
https://imslp.org/wiki/Symphony_No.45_in_F-sharp_minor,_Hob.I:45_(Haydn,_Joseph)

Take pages 3–9 only (page 1–2 are front matter) into a new PDF and run:

Audiveris.exe -batch -export -save -output <dir> -- haydn-pages-3-9.pdf

All 7 sheets reach PAGE. Exit code 1, no MusicXML.

I bisected this:

pages	sheets reaching PAGE	export
3–7	5 of 5	succeeds
3–8	6 of 6	succeeds
3–9	7 of 7	fails
9 alone	1 of 1	succeeds

So page 9 triggers it only in combination with the preceding sheets, not on its own. Page 9
is the first in the book whose systems hold three different staff counts (book.xml gives
<part> counts per <system> of 4, 5 and 6 on that sheet); pages 3–7 are uniformly 6 and
page 8 has two distinct counts.

Actual

Sheets 1–6 reload, sheet 7 does not:

INFO  SheetStub.java:1000 | Loaded /sheet#1 ... Loaded /sheet#6
WARN  SheetStub.java:1002 | Error in loading sheet structure javax.xml.bind.UnmarshalException
javax.xml.bind.UnmarshalException: null
	at com.sun.xml.bind.v2.runtime.JaxBeanInfo.invokeUnmarshallCallback(JaxBeanInfo.java:571)
	at com.sun.xml.bind.v2.runtime.JaxBeanInfo.invokeAfterUnmarshalMethod(JaxBeanInfo.java:562)
Caused by: java.lang.NullPointerException: Cannot read the array length because "this.sequences" is null
	at org.audiveris.omr.run.RunTable.afterMarshal(RunTable.java:339)
	at org.audiveris.omr.run.RunTable.afterUnmarshal(RunTable.java:359)

Audiveris then tries to recover, and the recovery itself fails:

INFO  SheetStub.java:1003 | Trying to restart from binary
WARN  DataHolder.java:166 | Error reading data from BINARY.png
java.nio.file.FileSystemAlreadyExistsException: null
	at jdk.zipfs/jdk.nio.zipfs.ZipFileSystemProvider.newFileSystem(Unknown Source)
	at org.audiveris.omr.util.ZipFileSystem.open(ZipFileSystem.java:111)
	at org.audiveris.omr.sheet.Book.openBookFile(Book.java:1840)
	at org.audiveris.omr.sheet.Book.openSheetFolder(Book.java:1856)
	at org.audiveris.omr.sheet.DataHolder.getData(DataHolder.java:143)
	at org.audiveris.omr.sheet.SheetStub.grabBinaryTable(SheetStub.java:1101)
	at org.audiveris.omr.sheet.SheetStub.resetToBinary(SheetStub.java:1471)
	at org.audiveris.omr.sheet.SheetStub.getSheet(SheetStub.java:1004)
	at org.audiveris.omr.score.Score.getPage(Score.java:483)

Leaving a null sheet, which surfaces as:

WARN  CLI.java:956 | Exception occurred java.lang.NullPointerException:
  Cannot invoke "org.audiveris.omr.sheet.Sheet.getPages()" because "sheet" is null
	at org.audiveris.omr.score.Score.getPage(Score.java:485)
	at org.audiveris.omr.score.Score.getPages(Score.java:621)
	at org.audiveris.omr.sheet.rhythm.Voices.refineScore(Voices.java:343)
	at org.audiveris.omr.sheet.Book.reduceScores(Book.java:2101)
	at org.audiveris.omr.sheet.Book.transcribe(Book.java:2633)
	at org.audiveris.omr.sheet.Book.export(Book.java:593)

Expected

A book whose sheets all reached PAGE should export.

Notes

1. RunTable.afterUnmarshal (line 359) calls afterMarshal (line 339), which dereferences
   sequences. On this sheet sequences is null after unmarshalling — an empty or
   run-less RunTable is my guess, but I have not read the source.
2. The FileSystemAlreadyExistsException looks independently fixable: ZipFileSystem.open
   is asked for a filesystem on a book file that is already open at that moment, so
   resetToBinary can never succeed on a book being exported. Even if (1) is fixed,
   anything else that triggers resetToBinary mid-export will hit this.

I also see the getPages() NPE at a different sheet index depending on how many sheets
are in the book, over overlapping content, so I would not read too much into which sheet is
named in any single run.

Filed separately: a RHYTHMS-step NPE in Voices.refineSystem on the same score's later
pages.

[jdburrage]

A second, independent reproducer — different composer, era, instrumentation and engraver
from the Haydn, and smaller. Same environment as the original report (5.11.0, build
9e1e55cd, Windows 11, OpenJDK 25.0.3).

Itay Cohen, A small work for percussion ensemble — 14 pages, 191 KB, typeset by the
composer in MuseScore, freely downloadable from IMSLP as file #609413:
https://imslp.org/wiki/A_Small_Work_for_Percussion_Ensemble_(Cohen,_Itay)

Pages 1–2 are a title page and an instrumentation list, which are flagged invalid and
abort the export on their own, so remove them first and run the remaining 12:

Audiveris.exe -batch -export -save -output <dir> -- cohen-pages-3-14.pdf

All 12 sheets reach PAGE. Exit code 1. No MusicXML.

Sheets 1–5 reload during export, sheet 6 does not:

INFO  SheetStub.java:1000 | Loaded /sheet#1 ... Loaded /sheet#5
WARN  SheetStub.java:1002 | Error in loading sheet structure javax.xml.bind.UnmarshalException
Caused by: java.lang.NullPointerException: Cannot read the array length because "this.sequences" is null
	at org.audiveris.omr.run.RunTable.afterMarshal(RunTable.java:339)
	at org.audiveris.omr.run.RunTable.afterUnmarshal(RunTable.java:359)

The binary-restart fallback then fails as described in the original report — three
FileSystemAlreadyExistsException from ZipFileSystem.open on the book file that is
already open — leaving a null sheet:

WARN  CLI.java:956 | Exception occurred java.lang.NullPointerException:
  Cannot invoke "org.audiveris.omr.sheet.Sheet.getPages()" because "sheet" is null
	at org.audiveris.omr.score.Score.getPage(Score.java:485)
	at org.audiveris.omr.score.Score.getPages(Score.java:621)
	at org.audiveris.omr.sheet.rhythm.Voices.refineScore(Voices.java:343)
	at org.audiveris.omr.sheet.Book.reduceScores(Book.java:2101)
	at org.audiveris.omr.sheet.Book.transcribe(Book.java:2633)
	at org.audiveris.omr.sheet.Book.export(Book.java:593)

Consistent with the staff-count observation in the original report, this score's systems
also vary. <part> counts per <system>, per sheet, read from book.xml:

sheet  1  [4]      sheet  5  [3]      sheet  9  [4]
sheet  2  [3,4]    sheet  6  [3,4]    sheet 10  [4,5]
sheet  3  [4,5]    sheet  7  [4,5]    sheet 11  [4]
sheet  4  [4]      sheet  8  [4]      sheet 12  [3,4]

It is a percussion ensemble score for six players, so staves are omitted where players
rest — the same shape as the Haydn finale, arrived at for a completely different musical
reason.

Worth noting what is lost: recognition on this input is good. The .omr holds 43
PERCUSSION_CLEF inters at grades 0.776–0.783, plus 36 F_CLEF and 27 G_CLEF, and every
sheet reached PAGE cleanly. All of it is discarded at export.