Unable to modify annotation time in existing EAFs in 5.6

elstickles · 5 June 2019 21:56

I recently upgraded to 5.6 on Mac OS 10.14 and since then have had issues with editing EAFs that were created with previous versions of ELAN. Please note I’ve replicated this issue on multiple computers (all running OS 10.14).

The existing EAFs were created using a template and are linked to mp4s. The files open just fine, but when trying to modify an annotation TIME (not value) it doesn’t work. I’ve tried using all the methods described in the online manual (section 5.7.7): (a) selecting the region, right clicking the original annotation and selecting Modify annotation time; (b) the same method but using CTRL+ENTER; and © ALT-clicking and dragging the selection using the mouse. The region is selected but it does not actually modify the annotation time. The annotation also cannot be manually changed using the “Modify annotation time…” option.

What is particularly strange is that if you attempt to modify the annotation time, and then click Edit, the option to “Undo Modify Annotation Time” (aka CTRL-Z) is there. So it appears the software “thinks” the modification happened, even though it did not. If you save the file, close, and re-open it, no changes were saved. However, if you save and close the file with the region still selected, the selection region is still there on re-opening. (I’m happy to send screenshots or a screencap video if it helps to illustrate this.) I’ve tried various fixes like re-sizing the annotation grid and nothing happens.

You can modify the annotation value properly. It’s only the annotation time that won’t modify.

Notably, an EAF created in 5.6 using the template (which was created using an older version) has the same problem. However, creating a brand new EAF without the template does not have this problem. So the problem appears to be directly related to older EAFs and templates in the current version ELAN.

Here is an example log file. I opened one of the EAFs, attempted to modify an annotation time using the ALT-click and drag method, and saved it.

Jun 05, 2019 11:20:30 AM mpi.eudico.client.annotator.ELAN main
INFO:

@ELAN Launched

Jun 05, 2019 11:20:31 AM mpi.eudico.client.annotator.ELAN main
INFO: ELAN 5.6-FX
Java home: /Applications/ELAN_5.6-AVFX.app/Contents/PlugIns/Java.runtime/Contents/Home
Java version: 11.0.1
Runtime: 11.0.1+13
OS name: Mac OS X
OS version: 10.14
OS arch.: x86_64
User language: en
User home: /Users/elisestickles
User dir: /Applications/ELAN_5.6-AVFX.app/Contents/Java
Classpath: /Applications/ELAN_5.6-AVFX.app/Contents/Java/elan-5.6.jar:javafx-controls-11-mac.jar:xmlbeans-2.6.0.jar:commons-logging-1.2.jar:javafx-graphics-11-mac.jar:json-20160212.jar:jna-3.5.2.jar:httpclient-4.4.1.jar:guk-0.7.jar:activation-1.1.1.jar:javax.activation-api-1.2.0.jar:javafx-base-11-mac.jar:jlfgr-1.0.jar:slf4j-api-1.7.5.jar:lexan-api-0.9.jar:xercesImpl-2.11.0.jar:elan-5.5.jar:metadata-api-1.5.0.jar:staccato-1.0.0.jar:log4j-1.2.17.jar:mfsearch-1.5.7.jar:javafx-media-11-mac.jar:javafx-base-11.jar:AppleJavaExtensions-1.0.jar:commons-codec-1.9.jar:jaxb-api-2.3.1.jar:javafx-swing-11.jar:annot-search-lib-1.4.11.jar:vlcj-2.4.1.jar:xml-resolver-1.2.jar:commons-io-2.5.jar:bridj-0.7.0.jar:javafx-controls-11.jar:javafx-swing-11-mac.jar:xml-apis-1.4.01.jar:javafx-media-11.jar:annotation-schema-1.0.jar:annot-tools-1.1.12.jar:hsqldb-1.8.0.10.jar:xalan-2.4.1.jar:lexiconcomponent-1.6.jar:hunspell-bridj-1.0.4.jar:platform-3.5.2.jar:dx-1.7.jar:javafx-graphics-11.jar:jhall-2.0.0.5.jar:help.zip:httpcore-4.4.1.jar:im/nl.mpi.gim__V04.jar:im/nl.mpi.lookup__V1.0.jar:im/nl.mpi.lookup.CJKV__V03.jar:im/nl.mpi.lookup.IPA__V04.jar:jaxb-core.jar:jaxb-impl.jar
Library path: nativelib
Display info:
Screen 1 - isDefault:true, w:1280, h:800, bitDepth:32
Screen 2 - isDefault:false, w:1600, h:900, bitDepth:32
Main screen resolution:113 (w:1280, h:800)

Jun 05, 2019 11:20:31 AM mpi.eudico.client.annotator.prefs.PreferencesReader parse
INFO: Reading preferences: /Users/elisestickles/Library/Preferences/ELAN/elan.pfsx
External updater thread started
Jun 05, 2019 11:20:33 AM mpi.eudico.client.annotator.prefs.PreferencesReader parse
INFO: Preferences file does not exist: /Users/elisestickles/Library/Preferences/ELAN/shortcuts.pfsx
Jun 05, 2019 11:20:33 AM mpi.eudico.client.annotator.commands.ShortcutsUtil readCurrentShortcuts
INFO: Could not load the keyboard shortcut preferences file. The file does not exist or is not valid.
Open
Jun 05, 2019 11:20:34 AM mpi.eudico.client.annotator.prefs.PreferencesReader parse
INFO: Reading preferences: /Users/elisestickles/Dropbox/Tasha Elise Matt Jason/results/ELAN files/origami task ES/test.pfsx
Using AVFN Player for file:///Users/elisestickles/Desktop/10a_10.23.2017_TNL.mp4
Jun 05, 2019 11:20:34 AM nl.mpi.avf.player.AVFBaseMediaPlayer <init>
INFO: Media URL for AVFPlayer: file:///Users/elisestickles/Desktop/10a_10.23.2017_TNL.mp4
Jun 05, 2019 11:20:34 AM mpi.eudico.client.annotator.player.JAVFELANMediaPlayer logMediaInfo
INFO: JAVF Media Player:
File: file:///Users/elisestickles/Desktop/10a_10.23.2017_TNL.mp4
Has Video: true
Video Size: 1920 x 1080
Frame Duration: 33.366665 sec., Frame Rate: 29.970032
Media Duration: 00:06:50.475
Jun 05, 2019 11:20:34 AM mpi.eudico.client.annotator.commands.ClipMediaCA <init>
INFO: No clipping script found!
Jun 05, 2019 11:20:35 AM mpi.eudico.client.annotator.tiersets.TierSetUtil readTierSetsFromFile
INFO: Could not load the tier set file. The file does not exist or is not valid.
Jun 05, 2019 11:20:36 AM mpi.eudico.client.annotator.util.AvailabilityDetector detectFromJar
WARNING: No plug-in cmdi metadata file found in analyzer-gloss-0.5.jar
Jun 05, 2019 11:20:36 AM mpi.eudico.client.annotator.util.AvailabilityDetector detectFromJar
WARNING: No plug-in cmdi metadata file found in annotyzer-whitespace-split-0.7.jar
Jun 05, 2019 11:20:36 AM mpi.eudico.client.annotator.util.AvailabilityDetector detectFromJar
WARNING: No plug-in cmdi metadata file found in annotyzer-lexicon-0.5-compound.jar
Jun 05, 2019 12:57:57 PM mpi.eudico.client.annotator.prefs.PreferencesWriter encodeAndSave
INFO: Writing preferences: /Users/elisestickles/Dropbox/Tasha Elise Matt Jason/results/ELAN files/origami task ES/test.pfsx
Jun 05, 2019 12:57:59 PM mpi.eudico.client.annotator.prefs.PreferencesWriter encodeAndSave
INFO: Writing preferences: /Users/elisestickles/Dropbox/Tasha Elise Matt Jason/results/ELAN files/origami task ES/test.pfsx
Jun 05, 2019 12:57:59 PM mpi.eudico.client.annotator.prefs.PreferencesWriter encodeAndSave
INFO: Writing preferences: /Users/elisestickles/Dropbox/Tasha Elise Matt Jason/results/ELAN files/origami task ES/test.pfsx
Jun 05, 2019 12:57:59 PM mpi.eudico.client.annotator.prefs.PreferencesWriter encodeAndSave
INFO: Writing preferences: /Users/elisestickles/Dropbox/Tasha Elise Matt Jason/results/ELAN files/origami task ES/test.pfsx
Open
Jun 05, 2019 12:58:06 PM mpi.eudico.client.annotator.prefs.PreferencesReader parse
INFO: Reading preferences: /Users/elisestickles/Dropbox/Tasha Elise Matt Jason/results/ELAN files/origami task ES/10a_10.23.2017_TNL.pfsx
Using AVFN Player for file:///Users/elisestickles/Desktop/10a_10.23.2017_TNL.mp4
Jun 05, 2019 12:58:06 PM nl.mpi.avf.player.AVFBaseMediaPlayer <init>
INFO: Media URL for AVFPlayer: file:///Users/elisestickles/Desktop/10a_10.23.2017_TNL.mp4
Jun 05, 2019 12:58:06 PM mpi.eudico.client.annotator.player.JAVFELANMediaPlayer logMediaInfo
INFO: JAVF Media Player:
File: file:///Users/elisestickles/Desktop/10a_10.23.2017_TNL.mp4
Has Video: true
Video Size: 1920 x 1080
Frame Duration: 33.366665 sec., Frame Rate: 29.970032
Media Duration: 00:06:50.475
Jun 05, 2019 12:58:06 PM mpi.eudico.client.annotator.commands.ClipMediaCA <init>
INFO: No clipping script found!
Jun 05, 2019 12:58:07 PM mpi.eudico.client.annotator.prefs.PreferencesWriter encodeAndSave
INFO: Writing preferences: /Users/elisestickles/Library/Preferences/ELAN/elan.pfsx
Jun 05, 2019 12:59:20 PM mpi.eudico.server.corpora.clomimpl.dobes.EAF30Encoder save
INFO: /Users/elisestickles/Dropbox/Tasha Elise Matt Jason/results/ELAN files/origami task ES/10a_10.23.2017_TNL.eaf <---- XML output - EAF version: 3.0

elstickles · 5 June 2019 22:36

Update: I created a new file in 5.6 and have replicated the issue described above. Any dependent ‘Included In’ tier cannot have its annotation times modified. It appears that this may be an issue with 5.6 in general, not just older files opened in 5.6. I also think this may be tier attribute-specific, because the default level tier annotation times CAN be modified. However, dependent tiers with the time-aligned “Included In” attribute cannot have their annotation times modified. I haven’t tested other tier attributes.

hasloe · 6 June 2019 11:48

I’m afraid this problem can be reproduced and it appears to be an unnoticed side-effect of a fix of another problem with “Included In” tiers in ELAN 5.5. Most unfortunate.
Editing of Included In annotations still works in ELAN 5.4 (but that version doesn’t work well, or not at all, on macOS 10.14). We’ll try to fix this problem in the next release.

elstickles · 6 June 2019 20:07

Hi Han,

Thanks for confirming this is a reproducible issue for you. Incidentally we’ve now reproduced it on a PC as well.

Do you have a timeline for when the fix will come out? Unfortunately until then, this makes ELAN unusable for my research group. As you said, 5.4 doesn’t work on 10.14 and reverting back to a prior OS version isn’t really possible. (Do you know the most current version of mac OS it does work on?)

hasloe · 8 June 2019 23:54

There was no new version planned soon, but I guess we have to try to get a bug fix release out this week.

Until then maybe you can try this temporary fix:

download this modified ELAN 5.6 library from this temporary url:
elan-5.6.jar
save it somewhere on your disc (e.g. the Downloads folder)
in the Finder, locate the folder where ELAN_5.6-AVFX is installed, right click ELAN_5.6-AVFX and choose Show Package Contents from the context menu
navigate to Contents/Java, copy or move the new elan-5.6.jar file to this folder, replacing the old version
return to the normal folder view of Finder and launch ELAN 5.6-AVFX again