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From 12/15/2009 to 01/13/2010

01/13/2010

10:12 PM Bug #4668: Documentation for event-state module
created wiki page with explanation and example code:
https://kepler-project.org/developers/reference/using-event-stat...
ben leinfelder
03:24 PM Bug #4668 (Resolved): Documentation for event-state module
Need developer-level documentation for how to use the even-state module in other modules. ben leinfelder
06:38 PM Bug #4505: NPE from Semantic Search
fixed in r22488, semantic search can return results now. Derik Barseghian
04:31 PM Bug #4505: NPE from Semantic Search
The error for this is now:
java.lang.NullPointerException
at org.kepler.objectmanager.ActorMetadata.getActorAsNamedO...
Derik Barseghian
04:36 PM Bug #4194: Kepler should have the Continous and Modal domains
I can at least get the Continuous domain in place for 2.0.0.
I was looking at how to do this, and I've not yet found...
Christopher Brooks
04:24 PM Bug #4659: Importing run gives a ClassCastException
fixed in r22486.
problem was in WorkflowRun convertStringToWorkflowRun -- derivedFrom attribute was being created as...
Derik Barseghian
04:12 PM Bug #4629: Undo doesn't roll LSID revision
Problems with LSIDs not getting updated properly need to be solved before 2.0.0 Aaron Aaron
03:58 PM Bug #4503: Suggest Similar Components gives an error
Maybe we should disable this feature for 2.0? Was it in 1.0? Chad Berkley
03:51 PM Bug #4347: Reminder "bug" for manual testing before 2.0 release
will rework this into a release bug Chad Berkley
03:46 PM Bug #4439: reporting displays output for a different actor
oh, neat! ben leinfelder
03:45 PM Bug #4439: reporting displays output for a different actor
It now prints an error message to stdout and in the report for any unresolved references. Daniel Crawl
03:37 PM Bug #4373: Copyright Statements are Inconsistent
Will do this as part of the release process. Chad Berkley
03:36 PM Bug #4317: KAR's dependencies on modules need to be included in KAR metadata
this can be pushed to post 2.0 Chad Berkley
03:35 PM Bug #4483: Module dependencies in MoML files
This visual icon is in the tree. Downloading now works when you right click on the item and tell it to get the depen... Chad Berkley
03:31 PM Bug #1750: Allow KAR files to include jar/class files
This can be talked about further after the 2.0 release. Chad Berkley
03:30 PM Bug #4322: Attempting to save changes to a workflow saved in a KAR file fails
Fix this after 4515 is done. Chad Berkley
03:28 PM Bug #4341: rearrange the actors module into smaller modules
pushing this to post-2.0. At this point, I don't think 2.0 should require this. Chad Berkley
03:25 PM Bug #4304: Progress monitor is blank when authenticating for KAR upload
this should be fixed with the kar saving functionality that aaron is adding (bug 4515) Chad Berkley
02:52 PM Bug #4642: memory usage & slowdowns
I've done some refactoring of the WRM so that I'm no longer creating so many runs so frequently -- hopefully this wil... Derik Barseghian
02:51 PM Bug #3976: Update Documentation for 2.0 release
Assigning to Debi. Chad Berkley
02:51 PM Bug #4316: re-evaluate how kars are managed in the build and runtime
KARs will not be checked into SVN for the forseable future. Closing this bug. We can reopen it at a later time if t... Chad Berkley
02:49 PM Bug #4667 (In Progress): New documentation on modules and extension points for modules
Should include information on the config system, karentryhandlers, viewpanes,
adding icons to the config, etc. See ...
Chad Berkley
02:45 PM Bug #4666 (Resolved): identify problems with converting .kepler-1.0 to .kepler-2.0
Need to go through the kepler 1.0 version of .kepler and identify any problem areas that might crop up in converting ... Chad Berkley
02:39 PM Bug #4665 (Resolved): Add unit tests for kar functionality
Build a junit test framework for at least the basic functionality of the KAR subsystem. Chad Berkley
02:37 PM Bug #4664 (Resolved): Fix and/or remove broken unit tests
Go through the unit test suite and get all tests to run. remove any tests that are no longer relevant and make the r... Chad Berkley
02:33 PM Bug #4506: Exception is thrown during workflow execution
Seems like a workflow bug, not a kepler bug. Chad Berkley
02:30 PM Bug #4482: JRE Exception Access Violations
probably machine specific. not a kepler bug. Chad Berkley
02:28 PM Bug #4350: Integrity constraint violation - no parent SYS_FK_59 table - during _first_ startup
The cache directory just needs to be cleaned. Chad Berkley
02:09 PM Bug #4340: Resolve KAR file/module format
We have now done this, as far as the 2.0 release is concerned. the KAR and module format will remain separate with k... Chad Berkley
12:28 PM Bug #4634: run archive causes NPE when building local repository
Oh, the part about archives not showing up is from bug 4559. This might have gotten fixed by something else along th... Oliver Soong
12:06 PM Bug #4634: run archive causes NPE when building local repository
Disclaimer: I haven't used the Build button often.
I just tried this on r22478, and don't get the error, but if the...
Derik Barseghian
12:17 PM Bug #4587: Assure a clean cache when module configuration changes
Fixed in r22479. Sean Riddle
10:41 AM Bug #4179: ant jar does not include configs/
I found another bug (feature maybe?) with the jar task. the resources/configuration directory gets put at the root o... Chad Berkley

01/12/2010

11:33 PM Bug #4549: String Replace actor "remembers" previous execution values
Unfortunately, this fix causes one of the tests to fail:
------------------ testing $PTII/ptolemy/actor/lib/string/t...
Christopher Brooks
11:11 PM Bug #4549: String Replace actor "remembers" previous execution values
changed in the ptolemy code to not fire the old token if a new one did not exist ben leinfelder
10:15 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I have looked into the CommandLine.java class more with Oliver Soong, and am going to try to hook process so that one... David Welker
08:24 PM Bug #4311: Build system appears to lock if there is a conflict upon update
Fixed. Now, modules that have local modifications are not updated and an appropriate WARNING is given.
As far as Oli...
David Welker
05:18 PM Bug #4663: Tag shows up in workflow moml when it shouldn't
I suspect this is to do with the building of the KAR, probably with the way the workflow is fetched out of the Object... Derik Barseghian
04:54 PM Bug #4663 (Resolved): Tag shows up in workflow moml when it shouldn't
This may not be a tagging bug but a bug in a provenance query or in KAR building -- sometimes a tag that shouldn't be... Derik Barseghian
05:15 PM Bug #4559: local repositories not showing up in components tree
At this point, KAR files in local repositories are not ending up in the components tree when they are first added. T... Oliver Soong
05:10 PM Bug #4560: can't remove local repositories
And closing. Oliver Soong
05:09 PM Bug #4560: can't remove local repositories
This seems to work now. Oliver Soong
05:04 PM Bug #4570: dangling file handle for KARs
Ben said to do this. Oliver Soong
04:16 PM Bug #4656: Build system needs javadocs
I added javadocs to all build-area classes. Did some minor refactoring and
reformatting as well. Rendered Javadocs ...
Chad Berkley
04:11 PM Bug #4662 (Resolved): roll revision vs. new object ID
My current auth namespace is 3371. I have a file with an old auth namespace of 1347. If I open the XML file, view L... Oliver Soong
11:16 AM Bug #4660 (Resolved): Clicking in a section header highlights all the text.
I have a section header with some text in it and I want to change that text. If I click on it, it highlights all of ... Oliver Soong

01/11/2010

05:49 PM Bug #4659: Importing run gives a ClassCastException
I don't think it's related, but I'll keep that in mind when I look into this.
To replicate:
- change-to and launch ...
Derik Barseghian
01:44 PM Bug #4659: Importing run gives a ClassCastException
The could be from my fix to bug #4547
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4547
The change is that Doc...
Christopher Brooks
12:29 PM Bug #4659 (Resolved): Importing run gives a ClassCastException
If you try to Open Archive a KAR containing a workflow run that needs to be added to provenance, you get a ClassCastE... Derik Barseghian
12:26 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
I changed this around a bunch so it is now done in the GUI instead of on kepler startup. When a module-dependencies:... Chad Berkley
08:39 AM Bug #4439: reporting displays output for a different actor
I'm thinking you'd still want the report to render if al but one reference were valid, right? Maybe just a warning th... ben leinfelder
08:36 AM Bug #4439: reporting displays output for a different actor
Why not just check that everything mentioned in the ROML exists just before you create the report (i.e., after execut... Oliver Soong
12:39 AM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
no difference, I simply missed checking in part of the fix initially Derik Barseghian

01/10/2010

11:03 PM Bug #4547: documentation for file parameter includes an error
Fixed. Changed DocAttribute.description from a StringParameter to a StringAttribute so that Kepler does not report er... Christopher Brooks
10:24 PM Bug #4439: reporting displays output for a different actor
i suppose we could be listening for the MOML change request that deletes actors/ports/parameters that are referenced ... ben leinfelder
10:21 PM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
what was the difference for linux? ben leinfelder

01/08/2010

06:42 PM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
fixed in r22437. Derik Barseghian
06:27 PM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
r22436 fixed this on my mac build, but it's not working on linux... Derik Barseghian
03:32 PM Bug #4439: reporting displays output for a different actor
I've updated provenance to handle these types of renames.
It might be nice if reporting displayed an error or warnin...
Daniel Crawl
02:16 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I'm not clear why option 2 is so complicated. Just pass stdin, stdout, and stderr from svn to ant. I don't expect a... Oliver Soong
01:49 PM Bug #4311: Build system appears to lock if there is a conflict upon update
If an error is printed, I'd be fine with it. Right now, it appears to hang and does not give any further output. Chad Berkley
01:41 PM Bug #4311: Build system appears to lock if there is a conflict upon update
A couple of things. First, there are two alternative things we could mean by "fixing" this issue: (1) Print out the e... David Welker
12:45 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I still don't think it really affects the user experience, but it's happened to me enough times to be annoying so I c... Chad Berkley
12:38 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I was curious what the basis of your opinion that this should be done before 2.0 is? This is functionality to make li... David Welker
10:15 AM Bug #4311: Build system appears to lock if there is a conflict upon update
This bug has happened to me exactly the way that Oliver has described on many occasions. It should be fixed prior to... Chad Berkley
09:52 AM Bug #4311: Build system appears to lock if there is a conflict upon update
The problem is that it never fails to complete. Normally on a conflict, svn outputs some information and blocks for ... Oliver Soong
01:46 PM Bug #4653: error message says "data cloumn"
search. replace. done. ben leinfelder
01:37 PM Bug #4655: data packages are suddenly unusable
dan fixed it ben leinfelder
12:39 PM Bug #4655: data packages are suddenly unusable
the cached data files are set as a data source for HSQL tables (SET TEXT....SOURCE) - but the path to the hsqldb was ... ben leinfelder
12:53 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
tagged my current work here: https://code.kepler-project.org/code/kepler/tags/berkley-20100108-checkpoint-kar_can_dow... Chad Berkley
12:49 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
There should always be user input when downloading new modules. Imagine that you are running the Kepler suite, then ... Aaron Aaron
12:40 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
Couple more issues here:
* I should have used the MANIFEST/dependsOnModule attribute instead of including a modules....
Chad Berkley
12:19 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
How does appending modules to modules.txt ensure the same environment that an actor was running in?
This is going to...
David Welker
11:59 AM Bug #4516: Module Manager needs ability to install modules needed by KARs
The active modules.txt file is now appended with any information from the kar's modules.txt file. Note that this cou... Chad Berkley
10:58 AM Bug #4516: Module Manager needs ability to install modules needed by KARs
Kar files can now include a modules.txt file which will be processed by the ModuleDownloader. Any modules/suites in ... Chad Berkley
11:02 AM Bug #4656 (Resolved): Build system needs javadocs
The build system is lacking a lot of documentation. Javadocs should be added for (at least) all public methods and c... Chad Berkley
10:19 AM Bug #4108: Do more extenstive testing before designating a revision of Ptolemy as stable
I don't think this bug should be closed. I'm changing it to be a lower priority but reopening it. I think that ther... Chad Berkley

01/07/2010

08:12 PM Bug #4311: Build system appears to lock if there is a conflict upon update
Are you saying that when the update failed to complete, it did not say why? That is unusual. Can you reproduce this e... David Welker
07:57 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I'm not so sure it's a good idea to ignore this. This happened to Mark, Regetz, and me. None of us had made any loc... Oliver Soong
07:24 PM Bug #4311: Build system appears to lock if there is a conflict upon update
The solution to this problem is not in the build system. You should do the update manually if you have made changes. David Welker
07:59 PM Bug #4388: remove the ptII module
There is no good way to remove the ptII suite without changes to the ptolemy module. This is not currently in the car... David Welker
07:52 PM Bug #4281: ant update produces message about running svn cleanup
I agree that this bug should be closed. "ant update" is a convenience method which allows one to avoid having to run ... David Welker
07:47 PM Bug #4280: ant task fails under Windows
Again, "ant task" is a convenience short cut for:
ant -f kepler-tasks.xml
Therefore, I do not intend on devoting an...
David Welker
07:44 PM Bug #4264: ant task fails if there are java compilation errors
"ant task" is a convenience method. It never needs to be invoked.
If "ant task" fails, the solution is to type:
ant...
David Welker
07:40 PM Bug #4260: Add a test suite for the build system
I think this is overkill and not a good use of resources. Problems in the build system tend to be detected immediatel... David Welker
07:22 PM Bug #4108: Do more extenstive testing before designating a revision of Ptolemy as stable
Additional testing before designating a version of Ptolemy as "stable" is unnecessary. Closing this bug. David Welker
07:21 PM Bug #4202: typos in modules.txt are ignored
The contents of modules.txt is now verified. Missing/mispelled modules now cause an error message to appear. David Welker
07:18 PM Bug #4353: Update publishing to allow for patches.
This is now implemented. David Welker
07:14 PM Bug #4351: ant netbans fails due to missing file
This bug no longer occurs. David Welker
07:12 PM Bug #4286: Changes to the GUI before 2.0
There are only minor changes left before 2.0. This bug is no longer needed. David Welker
07:03 PM Bug #4082: New user guide section on modules/module manager
Please assign bugs to welker4kepler@gmail.com when assigning bugs to me only.
I have documented module manager funct...
David Welker
07:00 PM Bug #4382: Remove switching between kepler and ptolemy
It is no longer possible to launch Ptolemy from the Kepler module manager. This reinforces the separateness of the tw... David Welker
06:58 PM Bug #4650: module manager tries to download already downloaded modules
Modules that are retrieved are not removed from the available modules pane. Instead, they are added to the "Downloade... David Welker
11:20 AM Bug #4650 (Resolved): module manager tries to download already downloaded modules
After downloading a module, that module should be removed from the "available modules" list. If a user tries to down... Chad Berkley
06:23 PM Bug #4655 (Resolved): data packages are suddenly unusable
For some reason, EML 2 Dataset actors are not outputting any tokens for most output formats. The data exists at .kep... Oliver Soong
06:09 PM Bug #4654: searching KNB through Kepler returns many console errors and caching fails
It's looking like I managed to completely screw up my cache. A clean-cache fixed things.
Basically, I was signing i...
Oliver Soong
05:44 PM Bug #4654 (Resolved): searching KNB through Kepler returns many console errors and caching fails
This is at r22407 under linux. Things seem to work, but the cache content is all blank (files are all of size 0). Oliver Soong
05:13 PM Bug #4653 (Resolved): error message says "data cloumn"
The data cloumn didn't match head column Oliver Soong
04:55 PM Bug #4652 (Resolved): clicking rows in the wrm no longer updates the report designer/viewer
If I have multiple entries in the wrm and I click on different rows, the report designer and viewer no longer automat... Oliver Soong
10:01 AM Bug #4516: Module Manager needs ability to install modules needed by KARs
I've now split the module manager into two modules. module-manager now has basic classes for downloading modules. m... Chad Berkley

01/06/2010

11:36 AM Bug #4161: Develop kepler workflow execution engine
installed on my local system - did a roundtrip:
-upload workflow+report
-schedule
-wait
-view PDF report when complet...
ben leinfelder

01/05/2010

04:08 PM Bug #4161: Develop kepler workflow execution engine
stylesheet issue on the Metacat side of things -- now fixed. ben leinfelder
11:40 AM Bug #4161: Develop kepler workflow execution engine
script-based execution still works. There's a slight problem on the Metacat side for the first MOML DTD...but that's ... ben leinfelder
03:09 PM Bug #4648 (Resolved): Create classes to find and display any available documentation for installed modules or suites.
Create classes to find and display the available documentation for installed modules or suites. debi staggs
03:06 PM Bug #4647 (Resolved): Write documentation for Reporting in the style of Kepler Docs
Write the user documentation for the WRP suite, using the same style as the rest of the Kepler documentation. debi staggs
11:31 AM Bug #4538: problems with KARs that contain tags from default ontologies
(In reply to comment #2)
> this looks wrong:
> <property name="semanticType" class="org.kepler.sms.SemanticType"
> va...
Sean Riddle
10:09 AM Bug #4538: problems with KARs that contain tags from default ontologies
this looks wrong:
<property name="semanticType" class="org.kepler.sms.SemanticType"
value="urn:lsid:lsid.ecoinformati...
ben leinfelder
10:05 AM Bug #4453: tags don't show up in snow leopard (10.6)
this is working for me on snow leopard ben leinfelder
10:04 AM Bug #4480: can't view more than one of workflow editor, report designer, and report viewer at a time
retargeting to post-2/wrp ben leinfelder
09:43 AM Bug #4618: First export of a run doesn't yield KAR with ROML
in the name of upcoming code freeze, I'm thinking this can be closed. ben leinfelder

01/04/2010

02:47 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
I added a karEntryHandler for modules.txt files. I'm going to add a method to the module manager sot hat the entryHa... Chad Berkley

01/03/2010

12:26 PM Bug #4547: documentation for file parameter includes an error
Viewing the documentation for FileParameter works fine in the ptII tree,
but fails in Kepler, probably because of som...
Christopher Brooks

12/29/2009

11:45 AM Bug #4603: Make limited changes to tagging in preparation for initial release
Fixed as of r22287. Sean Riddle
07:59 AM Bug #4547: documentation for file parameter includes an error
Parsing the description is throwing an error - perhaps it's trying to substitute values or $ID?
Snippet from the File...
ben leinfelder

12/27/2009

11:14 AM Bug #4547: documentation for file parameter includes an error
also in StringParameter.
It's not in the actor moml...so it must be in the action that is displaying the documentation
ben leinfelder
11:10 AM Bug #4522: Folder not found in library index
just tried this (r22284) and it seems to be working. ben leinfelder
10:48 AM Bug #4439: reporting displays output for a different actor
More testing makes this look related to provenace:
I create a simple [runnable] workflow so that I can execute it to ...
ben leinfelder
09:51 AM Bug #4618: First export of a run doesn't yield KAR with ROML
Would you just bump the run revision (entityId)? But then wouldn't that mean it's a different "run" rather than the s... ben leinfelder
09:23 AM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
er, close ben leinfelder
09:23 AM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
removed PTree override in reporting. all better now! ben leinfelder
08:56 AM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
there's a PTree override in the reporting module...but I don't see it being referenced in that module. Looking into r... ben leinfelder

12/24/2009

01:27 PM Bug #4467: WRP - restarting/reopening Kepler throws error
I'm closing this since I can't ever get it to happen for me and there's been so much change since it was entered that... ben leinfelder
01:23 PM Bug #4534: add extra space before section headers when BREAK_BEFORE is false
added some padding above the section header text ben leinfelder
01:16 PM Bug #4480: can't view more than one of workflow editor, report designer, and report viewer at a time
we've changed it a bit: two views - the "reporting" view has 2 tabs: layout and instance. but you do still have to sw... ben leinfelder
01:13 PM Bug #4614: right click -> Open on an existing run adds an entry to the wrm
i don't see this happening in my build as of today (12-24-2009) ben leinfelder
01:09 PM Bug #4600: Changing workflow & running causes "execution history not found" message to appear in report viewer
I've not gotten this error. I had seen the blank report error from before.
With the latest fix, this should not be ha...
ben leinfelder
01:07 PM Bug #4599: changing Expression and running problematic workflow generates blank report
okay - now when the LSID is changed, the layout manager listens for the change event and reassociates the layout with... ben leinfelder
11:13 AM Bug #4638: ant clean-all no longer works
just tried it at r22278 and it works ben leinfelder

12/18/2009

07:45 PM Bug #4642 (New): memory usage & slowdowns
I just hit a big slowdown caused by OOM problems. This bug is mostly a place to put down some of the stuff I found o... Oliver Soong
03:18 PM Bug #4639 (New): add support for -Drev to ant change-to
Doesn't happen very often, but I often am not checking out the head revision, and so it would be nice if ant change-t... Oliver Soong
01:54 PM Bug #4630: creating and changing relations don't trigger LSID bump
For now I've allowed manually bumping the LSID revision and Object ID from the LSID Viewer panel so there's at least ... Aaron Aaron
12:19 PM Bug #4599: changing Expression and running problematic workflow generates blank report
Until this gets fixed, a workaround is to give the workflow an LSID from the local Kepler install. Basically, delete... Oliver Soong
12:09 PM Bug #4632: problems when loading a KAR, changing the workflow, then re-saving the KAR
This actually looks great right now. It seems to clear all the test cases. Oliver Soong
11:34 AM Bug #4638: ant clean-all no longer works
It works at r22253. Oliver Soong
11:33 AM Bug #4638 (Resolved): ant clean-all no longer works
This is with modules\build-area at r22254. ant clean-all and ant clean-cache both fail:
build-area\build.xml:4: ...
Oliver Soong

12/17/2009

08:01 PM Bug #4633: LSID conflicts
The logic for querying a new namespace from an Authority in the event that the recorded object IDs and revisions have... Aaron Aaron
06:47 PM Bug #4514: Files are being saved in the Kepler installation directory
InstanceAuthNamespace now gets saved into the persistent Kepler core module directory. LastObjectID file is no longe... Aaron Aaron

12/16/2009

11:09 AM Bug #4619: WorkflowRuns not showing inside KARs in library
r22211 fixes problem in comment#5. Derik Barseghian
10:57 AM Bug #4630: creating and changing relations don't trigger LSID bump
retargeting to 2.0 ben leinfelder
10:40 AM Bug #4571: report "lost" from KAR
Tried to "loose" the ROML - it just won't go away! Closing... ben leinfelder

12/15/2009

07:32 PM Bug #4633: LSID conflicts
LSIDGeneration and LSID Revision updates are now being recorded. The LSID_GENERATOR table still needs to be moved to... Aaron Aaron
03:25 PM Bug #4578: tracking bug for changes to .kepler
I have removed the use of the AuthNamespace from the .kepler directory structure.
The cache directory is now
~/.kep...
Aaron Aaron
12:15 PM Bug #4587: Assure a clean cache when module configuration changes
I'll work on getting this working. Chad Berkley
11:45 AM Bug #4338: need to review usability and gui of module manager
I tried the MM again from a clean build. I was able to change-to the kepler-1.0.0 suite, however there are some prob... Chad Berkley
08:49 AM Bug #4473: Add WRM to bottom of report viewer for navigation
I'm really liking this the more I interact with it.
I even like how you can "open" a row in a new window if you do wa...
ben leinfelder
08:47 AM Bug #4468: Report Viewer - message to run workflow first
Since we're not refreshing the viewer when you switch views (now a tab) the only time it comes up is when you use the... ben leinfelder
 

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