[WIP] Fix field formatter save actions throwing exception on autosave by Siedlerchr · Pull Request #5010 · JabRef/jabref

Siedlerchr · 2019-05-30T16:24:19Z

In my opinion this is an ugly hack but still the only option without violating our architecture.
Problem is that the autocompleter has an input binding which is triggered whenever setField in BibEntry is called, in this case part of the apply save actions.
On autosave we have a Background thread in the BackupoManager which executes the saveDatabaseAction which itself executes the save actions.

Exectuted in a background thread:

jabref/src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java

Lines 120 to 124 in e83680f

    
           Charset charset = bibDatabaseContext.getMetaData().getEncoding().orElse(preferences.getDefaultEncoding()); 
        
           SavePreferences savePreferences = preferences.loadForSaveFromPreferences().withEncoding 
        
                   (charset).withMakeBackup(false); 
        
           new BibtexDatabaseWriter(new AtomicFileWriter(backupPath, savePreferences.getEncoding()), savePreferences) 
        
                   .saveDatabase(bibDatabaseContext);

jabref/src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java

Lines 170 to 177 in e83680f

    
           // Write database entries. 
        
           List<BibEntry> sortedEntries = getSortedEntries(bibDatabaseContext, entries, preferences); 
        
           List<FieldChange> saveActionChanges = applySaveActions(sortedEntries, bibDatabaseContext.getMetaData()); 
        
           saveActionsFieldChanges.addAll(saveActionChanges); 
        
           if (preferences.generateBibtexKeysBeforeSaving()) { 
        
               List<FieldChange> keyChanges = generateBibtexKeys(bibDatabaseContext, sortedEntries); 
        
               saveActionsFieldChanges.addAll(keyChanges); 
        
           }

Change in CHANGELOG.md described
Tests created for changes
Manually tested changed features in running JabRef
Screenshots added in PR description (for bigger UI changes)
Ensured that the git commit message is a good one
Check documentation status (Issue created for outdated help page at help.jabref.org?)

Fixes #4958

tobiasdiez

I think we need a generic solution for this. Otherwise we run consistently in these threading issues and in the long term it's not a reliable solution to extract certain things that need to run on the javafx thread due to the bindings.

I would propose to create methods bindOnUI(Property A, Property B) and bindBidirectionalOnUI in BindingsHelper which bind A and B but changes are propagated on the JavaFX thread. The implementation probably needs to copy the builtin classes and change the update mechanism:
https://github.com/javafxports/openjdk-jfx/blob/develop/modules/javafx.base/src/main/java/javafx/beans/property/ObjectPropertyBase.java#L234
https://github.com/javafxports/openjdk-jfx/blob/51f12edf47adfe0529e8cea10f399f4525687d27/modules/javafx.base/src/main/java/com/sun/javafx/binding/BidirectionalBinding.java#L599

26265bf Create pacific-science.csl (JabRef#5020) e6ff62e Update pravnik.csl & iso690-full-note-cs.csl (JabRef#5019) 8ab9362 Create turabian-9-author-date (JabRef#4796) 28c7021 Update west-european-politics.csl (JabRef#4900) 6d06e5e Create american-physical-society-et-al (JabRef#4974) 7472744 Create farmeconomia.csl (JabRef#5017) bd916df Create amerindia.csl (JabRef#5011) 28d176d Create law-technology-and-humans-journal-style.csl (JabRef#5015) a998aa5 Create kerala-journal-of-ophthalmology.csl (JabRef#5014) 8662257 Update journal-of-australian-strength-and-conditioning.csl (JabRef#5010) e28f06f Create clinical-management-issues.csl (JabRef#5008) abb92fb Create institut-francais-darcheologie-orientale-en.csl (JabRef#4870) f931c78 Update institut-francais-darcheologie-orientale.csl (JabRef#4869) 9d604ca Update journal-of-foraminiferal-research.csl 1191d07 add Journal of Foraminiferal Research (JabRef#5007) 0903e9d Update molecular-therapy.csl (JabRef#5009) 316d6c7 Update journal-of-alzheimers-disease.csl (JabRef#5006) 868a7ed Create journal-of-soil-science-and-plant-nutrition (JabRef#5005) 875ef81 Create universitat-bern-institut-fur-sozialanthropologie.csl (JabRef#4998) 1194b81 Create journal-de-la-societe-des-americanistes.csl (JabRef#4995) 1d2a472 Update international-energy-agency-organisation-for-economic-co-operation-and-development.csl (JabRef#4999) 02a26ef Update iso690-author-date-cs.csl (JabRef#5003) 165592c Create european-journal-of-entomology.csl (JabRef#5001) 4d587ca Create european-journal-of-anaesthesiology.csl (JabRef#5002) git-subtree-dir: src/main/resources/csl-styles git-subtree-split: 26265bf

26265bf Create pacific-science.csl (#5020) e6ff62e Update pravnik.csl & iso690-full-note-cs.csl (#5019) 8ab9362 Create turabian-9-author-date (#4796) 28c7021 Update west-european-politics.csl (#4900) 6d06e5e Create american-physical-society-et-al (#4974) 7472744 Create farmeconomia.csl (#5017) bd916df Create amerindia.csl (#5011) 28d176d Create law-technology-and-humans-journal-style.csl (#5015) a998aa5 Create kerala-journal-of-ophthalmology.csl (#5014) 8662257 Update journal-of-australian-strength-and-conditioning.csl (#5010) e28f06f Create clinical-management-issues.csl (#5008) abb92fb Create institut-francais-darcheologie-orientale-en.csl (#4870) f931c78 Update institut-francais-darcheologie-orientale.csl (#4869) 9d604ca Update journal-of-foraminiferal-research.csl 1191d07 add Journal of Foraminiferal Research (#5007) 0903e9d Update molecular-therapy.csl (#5009) 316d6c7 Update journal-of-alzheimers-disease.csl (#5006) 868a7ed Create journal-of-soil-science-and-plant-nutrition (#5005) 875ef81 Create universitat-bern-institut-fur-sozialanthropologie.csl (#4998) 1194b81 Create journal-de-la-societe-des-americanistes.csl (#4995) 1d2a472 Update international-energy-agency-organisation-for-economic-co-operation-and-development.csl (#4999) 02a26ef Update iso690-author-date-cs.csl (#5003) 165592c Create european-journal-of-entomology.csl (#5001) 4d587ca Create european-journal-of-anaesthesiology.csl (#5002) git-subtree-dir: src/main/resources/csl-styles git-subtree-split: 26265bf

26265bf Create pacific-science.csl (JabRef#5020) e6ff62e Update pravnik.csl & iso690-full-note-cs.csl (JabRef#5019) 8ab9362 Create turabian-9-author-date (JabRef#4796) 28c7021 Update west-european-politics.csl (JabRef#4900) 6d06e5e Create american-physical-society-et-al (JabRef#4974) 7472744 Create farmeconomia.csl (JabRef#5017) bd916df Create amerindia.csl (JabRef#5011) 28d176d Create law-technology-and-humans-journal-style.csl (JabRef#5015) a998aa5 Create kerala-journal-of-ophthalmology.csl (JabRef#5014) 8662257 Update journal-of-australian-strength-and-conditioning.csl (JabRef#5010) e28f06f Create clinical-management-issues.csl (JabRef#5008) abb92fb Create institut-francais-darcheologie-orientale-en.csl (JabRef#4870) f931c78 Update institut-francais-darcheologie-orientale.csl (JabRef#4869) 9d604ca Update journal-of-foraminiferal-research.csl 1191d07 add Journal of Foraminiferal Research (JabRef#5007) 0903e9d Update molecular-therapy.csl (JabRef#5009) 316d6c7 Update journal-of-alzheimers-disease.csl (JabRef#5006) 868a7ed Create journal-of-soil-science-and-plant-nutrition (JabRef#5005) 875ef81 Create universitat-bern-institut-fur-sozialanthropologie.csl (JabRef#4998) 1194b81 Create journal-de-la-societe-des-americanistes.csl (JabRef#4995) 1d2a472 Update international-energy-agency-organisation-for-economic-co-operation-and-development.csl (JabRef#4999) 02a26ef Update iso690-author-date-cs.csl (JabRef#5003) 165592c Create european-journal-of-entomology.csl (JabRef#5001) 4d587ca Create european-journal-of-anaesthesiology.csl (JabRef#5002) git-subtree-dir: src/main/resources/csl-styles git-subtree-split: 26265bf

Fix field formatter throwing exception on autosave

6f045e8

Fixes #4958

Siedlerchr added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label May 30, 2019

tobiasdiez requested changes May 31, 2019

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tobiasdiez removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Jul 11, 2019

Siedlerchr added the jabcon label Aug 24, 2019

stefan-kolb removed the jabcon label Aug 25, 2019

koppor added the status: waiting-for-feedback The submitter or other users need to provide more information about the issue label Aug 25, 2019

koppor changed the title ~~Fix field formatter save actions throwing exception on autosave~~ [WIP] Fix field formatter save actions throwing exception on autosave Aug 25, 2019

Siedlerchr mentioned this pull request Aug 28, 2019

Running Jabref with Java11 freezes system #5250

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This was referenced Sep 6, 2019

Exception after cleanup entries dialog with rename PDF option enabled #5108

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Wrapper classes for UI Lists etc that ensure updates on JavaFX thread #5289

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tobiasdiez closed this Sep 9, 2019

tobiasdiez deleted the fixautosaveThread branch September 9, 2019 20:05

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[WIP] Fix field formatter save actions throwing exception on autosave#5010

[WIP] Fix field formatter save actions throwing exception on autosave#5010
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fixautosaveThread

Siedlerchr commented May 30, 2019 •

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	Charset charset = bibDatabaseContext.getMetaData().getEncoding().orElse(preferences.getDefaultEncoding());
	SavePreferences savePreferences = preferences.loadForSaveFromPreferences().withEncoding
	(charset).withMakeBackup(false);
	new BibtexDatabaseWriter(new AtomicFileWriter(backupPath, savePreferences.getEncoding()), savePreferences)
	.saveDatabase(bibDatabaseContext);

	// Write database entries.
	List<BibEntry> sortedEntries = getSortedEntries(bibDatabaseContext, entries, preferences);
	List<FieldChange> saveActionChanges = applySaveActions(sortedEntries, bibDatabaseContext.getMetaData());
	saveActionsFieldChanges.addAll(saveActionChanges);
	if (preferences.generateBibtexKeysBeforeSaving()) {
	List<FieldChange> keyChanges = generateBibtexKeys(bibDatabaseContext, sortedEntries);
	saveActionsFieldChanges.addAll(keyChanges);
	}

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Siedlerchr commented May 30, 2019 •

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