Kepler

02/19/2010

05:01 PM Bug #4727: Cannot compile Ptolemy from IntelliJ

Yeah, I will be working on this. In the meantime, we can just patch the individual IDEs so that they work for everyone. David Welker

04:59 PM Bug #4727: Cannot compile Ptolemy from IntelliJ

This bug has cropped up again, this time also affecting Eclipse (and presumably NetBeans as well). The solution, acco... Sean Riddle

01:08 PM Bug #4815 (New): Need a target to build kepler-styles.jar

On kepler 1.0.0, there was a target to build kpelr-styles.jar from eml repository. However, it was removed from keple... Jing Tao

01:06 PM Bug #4807: GetMetadata does nothing

In eml module, duplicated parameters were removed on eml-settings.xsl and eml-identifiers.xsl. Use a new target in em... Jing Tao

02/18/2010

05:18 PM Bug #4812 (New): local repository KAR [right click]->Delete fails when file does not exist

Save a KAR to a local repository, then delete the file outside Kepler, then from the components tree right click the ... Oliver Soong

03:48 PM Bug #4804: copy/paste relation changes width from Auto to 1

I'm not 100% sure this is the same bug, but if I delete the actors and relation, then undo the change, the relation w... Oliver Soong

03:48 PM Bug #4798: Create parser for KAR XML specification

this is a 2.0 bug in that it is blocking the component search bug ben leinfelder

03:46 PM Bug #4798: Create parser for KAR XML specification

https://code.kepler-project.org/code/kepler/trunk/modules/core/src/org/kepler/kar/karxml/KARFile.xsd
is what exists ... ben leinfelder

12:51 PM Bug #4798: Create parser for KAR XML specification

As far as I know, no. That's a good point. I'll leave this open until there's some soft of official schema to check a... Sean Riddle

12:47 PM Bug #4798: Create parser for KAR XML specification

is there a complete XSD now? ben leinfelder

11:04 AM Bug #4798: Create parser for KAR XML specification

Wrote initial implementation. I'll leave this bug open for a day or two for interested parties (especially those invo... Sean Riddle

01:42 PM Bug #4811 (In Progress): No "Get Metadata" item on right-click menu after dragging an EML actor to the canvas

After dragging an EML actor from search result panel to canvas, there was a right-click menu item named "Get Metadata... Jing Tao

01:40 PM Bug #4810 (New): [right click]->Save Archive (KAR) on composite actor borks port attributes

Open the example MOML and save the composite actor as a KAR file. If you extract the MOML from the KAR, you'll see e... Oliver Soong

01:14 PM Bug #4808: ant clean-cache fails, NoClassDefFoundError, org/apache/commons/logging/LogFactory

This is fixed. Logging and third-party libraries should generally be kept out of the build. If you need a third-party... David Welker

12:51 PM Bug #4808: ant clean-cache fails, NoClassDefFoundError, org/apache/commons/logging/LogFactory

I am working on this bug now. It will be fixed shortly. David Welker

12:02 PM Bug #4808 (Resolved): ant clean-cache fails, NoClassDefFoundError, org/apache/commons/logging/LogFactory

Chris first reported this by e-mail, but I'm still seeing it. Aaron, svn says you put these lines in.
java.lang.N... Oliver Soong

12:51 PM Bug #4809: Kepler storing authenticated search results

I'm not sure the search is being performed on the server. All I know is I'm not being asked to authenticate again. Oliver Soong

12:45 PM Bug #4809: Kepler storing authenticated search results

this has long been the case for datasets that have already been downloaded/cached - if you restart Kepler you don't n... ben leinfelder

12:18 PM Bug #4809 (New): Kepler storing authenticated search results

From a clean cache, start Kepler and search using authenticated sources. Authenticate and Kepler will return search ... Oliver Soong

12:02 PM Bug #4807: GetMetadata does nothing

I can see a error on console:
[run] ERROR: 'jar:file:/home/tao/project/kepler/core/lib/jar/kepler-styles.jar!/style/... Jing Tao

11:49 AM Bug #4807 (Resolved): GetMetadata does nothing

Search for any data, right click on a search result, and select the only option, "GetMetadata". This does not seem t... Oliver Soong

11:44 AM Bug #4805: searching for data gives an NPE

It turned out that the NPE exception didn't affect the search result. But it still was annoying. We added a checking ... Jing Tao

02/17/2010

06:50 PM Bug #4793: Workflow Run Manager - clicking on row when provenance is off gives error

You also can't delete rows when provenance is off, because getDefaultProvenanceRecorder will return a Recording in th... Derik Barseghian

05:48 PM Bug #4797: Verify that multiple workflow/actor KARs work as expected

I have created a KAR file that contains all the actors in the actors module. I called it CoreActors.kar and attached... Aaron Aaron

04:11 PM Bug #4806 (New): add output port to Throw Exception

In some of my workflows, I have an actor that checks that certain components are installed and working before trying ... Oliver Soong

03:52 PM Bug #4805 (Resolved): searching for data gives an NPE

I searched for Kruger on both KNB and DEV using both authenticated and unauthenticated searches. I authenticated as ... Oliver Soong

03:34 PM Bug #4804: copy/paste relation changes width from Auto to 1

I can replicate this in Ptolemy
1. Right click on the relation and select "Configure". Note that the width is
set ... Christopher Brooks

03:26 PM Bug #4804 (Resolved): copy/paste relation changes width from Auto to 1

Drag 2 actors to the canvas and join them with a relation. Copy the actors and relation and immediately paste it. T... Oliver Soong

03:19 PM Bug #4801: out of memory

I suggest using JProfiler to track this down. They have a trial offer. Edward and I have licenses. I don't have th... Christopher Brooks

02:57 PM Bug #4801: out of memory

After getting the out of memory error, I generated a heap histogram, restarted Kepler, and generated another heap his... Oliver Soong

02:13 PM Bug #4801 (In Progress): out of memory

ERROR: RecordingException: Unable to query data table: out of memory
I opened tpc01, ran it, closed it, opened tpc... Oliver Soong

02:50 PM Bug #4803 (Resolved): Review the README file

Need to review the readme for factual accuracy and new content additions. Chad Berkley

02:44 PM Bug #4802: KARs in KeplerData/workflows are being parsed on startup

Ben can you email me the workflow that you're having problems with? Aaron Aaron

02:13 PM Bug #4802 (Resolved): KARs in KeplerData/workflows are being parsed on startup

When I launch Kepler with a clean cache but with a workflow sitting in my local workflow directory that uses protecte... ben leinfelder

02:43 PM Bug #4578: tracking bug for changes to .kepler

I would argue against having a task to clean the persistent directory. It's supposed to be persistent and not have t... Chad Berkley

02:35 PM Bug #4578: tracking bug for changes to .kepler

The kar directories that used to be in the cache are now in the KeplerData directory, so they are not deleted/rebuilt... Aaron Aaron

02:27 PM Bug #4578: tracking bug for changes to .kepler

ant clean-cache deletes .kepler/cache-2.0.0 in r23085 Derik Barseghian

02:12 PM Bug #4578: tracking bug for changes to .kepler

(In reply to comment #11)
> 'ant clean-cache' seems to not be deleting anything at the moment. shouldn't
> it?
Whoop... Derik Barseghian

02:06 PM Bug #4578: tracking bug for changes to .kepler

'ant clean-cache' seems to not be deleting anything at the moment. shouldn't it? ben leinfelder

01:55 PM Bug #4792: NPE from Eml200DataSource

Now giving an actual message for the NPE and throwing it up the chain. ben leinfelder

01:41 PM Bug #4792: NPE from Eml200DataSource

i'll take this. ben leinfelder

12:41 PM Bug #4800 (Resolved): CacheManager can not insert WorkflowRun into cache

When you export a run, CacheManager's insertObject cannot insert WorkflowRun entries into cache. This is because the ... Derik Barseghian

12:26 PM Bug #4789: multiport input to composite actor seems to only pass first token

Inside the composite, the relation between the multiport and the RExpression has width 1. I'm not sure how or why it... Oliver Soong

11:26 AM Bug #4789: multiport input to composite actor seems to only pass first token

If I listen to the multiport input on the RExpression inside the composite, I see one token on a single channel. If ... Oliver Soong

10:03 AM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I finally remembered that I can look directly at the provenance db while Kepler's running. I just deleted all the ru... Oliver Soong

02/16/2010

04:38 PM Bug #4799 (Resolved): "Login Anonymously" gave an error during the data search

After running Kepler, I typed the word "Datos" on the Search Data field and clicked search button. An Authentication ... Jing Tao

04:32 PM Bug #4798 (Resolved): Create parser for KAR XML specification

Create a parser for the new KAR XML format, for use especially when it is returned from a metacat query. Sean Riddle

03:51 PM Bug #4797 (Resolved): Verify that multiple workflow/actor KARs work as expected

The KAR system was written to allow for storing multiple actors/workflows inside the KAR. This has not been well tes... Aaron Aaron

02:20 PM Bug #4730: Kepler cannot run workflows stored in KAR files from the command-line.

Running kars is not supported except in a server configuration. The reason for this is that the kar is first sent to... Chad Berkley

02:18 PM Bug #4786: workflow file saved in KAR does not open when extracted

KeplerMetadataExtractor was using Document.getFirstChild() to get the rootNode when it should have been using Documen... Aaron Aaron

02/12/2010

11:59 PM Bug #4702: KAR to module conversion utility

Closing this bug because this feature is not needed at this time. David Welker

03:05 PM Bug #4702: KAR to module conversion utility

> This is an inappropriate conversation for this forum.
And what is the appropriate forum?
> This issue has already... Aaron Aaron

06:01 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I think it's too big to attach, so I've put it here:
http://www.nceas.ucsb.edu/~soong/kepler/provenance%20HSQLDB%20... Oliver Soong

05:22 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

Could I get a copy of the large db along with a list of steps performed to create it? Daniel Crawl

04:28 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

So I wiped my .kepler and KeplerData, started Kepler (to initialize these folders), and things ran "fast" (1-3 sec pe... Oliver Soong

04:04 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

Forgot to answer the question. Sort of. I can reproduce the 3000+ function calls, but they seem to resolve faster, ... Oliver Soong

03:41 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

That's correct and expected. recordContainerContents is initiated from changeExecuted, and it's recordContainerConte... Oliver Soong

03:26 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

If I run the workflow without accessing the data, and then change the targetYear, I only get 2 or 3 calls to changeEx... Daniel Crawl

08:54 AM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

It's in the Kruger SVN:
https://code.ecoinformatics.org/code/kruger/trunk/workflows/tpc09-plant-dynamics/tpc09-plant... Oliver Soong

08:43 AM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

Could you provide the workflow? Daniel Crawl

05:29 PM Bug #4795: RExpression & cache cleaning

Zactly. Oliver Soong

05:20 PM Bug #4795: RExpression & cache cleaning

Dan H. already had some code in there for managing "too long of strings" for the script input - long numeric arrays c... ben leinfelder

05:14 PM Bug #4795: RExpression & cache cleaning

We could do away with the .sav files. Ben, try this in R:
str <- paste("_data.frame_:", rawToChar(serialize(iris, ... Oliver Soong

04:36 PM Bug #4795: RExpression & cache cleaning

There are a few kinds of files generated by RExpression:
1. complex data transfer from one RExpression actor to anoth... ben leinfelder

04:22 PM Bug #4795: RExpression & cache cleaning

I've noticed this too, and it seems like a good idea to me.
If the RExpression actor put these files into the proven... Matt Jones

04:15 PM Bug #4795 (New): RExpression & cache cleaning

My .kepler cache bloats pretty quickly because of RExpression's temporary files. Can we have RExpression clear it's ... Oliver Soong

03:23 PM Bug #4792: NPE from Eml200DataSource

A better error message instead of NPE would be nice. Daniel Crawl

10:42 AM Bug #4792: NPE from Eml200DataSource

The workflow shouldn't run w/o the data.
What should be happening that isn't currently? Cleaner error? ben leinfelder

10:02 AM Bug #4792 (Resolved): NPE from Eml200DataSource

1. open https://code.ecoinformatics.org/code/kruger/trunk/workflows/tpc09-plant-dynamics/tpc09-plant-dynamics-woody.k... Daniel Crawl

03:16 PM Bug #4791: Actor names no longer have spaces

Sorry a clean-cache should fix this, I think my partially updated version had trouble due to the new cache location... Aaron Aaron

01:12 PM Bug #4791: Actor names no longer have spaces

Oh and also closing this bug Aaron Aaron

01:11 PM Bug #4791: Actor names no longer have spaces

Hey guys, yeah looks like the LibIndex was using the name of the Jar entry found in the manifest and not the name tha... Aaron Aaron

12:06 PM Bug #4791: Actor names no longer have spaces

I looked at this and it looks like the name of the actor is now derived from the name of the kar file. The name of t... Chad Berkley

01:27 PM Bug #4730: Kepler cannot run workflows stored in KAR files from the command-line.

This is actually two bugs.
Bug 1: Spaces in the paths on a workflow run does not work. I found this to be true an... Chad Berkley

12:25 PM Bug #4730: Kepler cannot run workflows stored in KAR files from the command-line.

The spaces aren't the issue. I can run this with no problem:
java -classpath build-area/lib/ant.jar:kepler.jar org.... Chad Berkley

11:49 AM Bug #4456: Workflow Run Manager in Report Viewer

This was fixed - the WRM is in the Report Designer view now and reports show when you click on run rows.
If you just ... Derik Barseghian

11:45 AM Bug #4793 (Resolved): Workflow Run Manager - clicking on row when provenance is off gives error

If you disable provenance and then click on a row in the WRM you get an error:
org.kepler.provenance.QueryExceptio... Derik Barseghian

11:42 AM Bug #4721: wrm gets exception when provenance turned off

Fixed in r23066.
However if you click on any row when prov is turned off you get an error. I'll file a bug for that. Derik Barseghian

02/11/2010

09:51 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

The function recordContainerContents is the cause of the slow behavior. It is called from _recordWorkflowContents wh... Oliver Soong

07:21 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I've tracked this down to the ProvenanceRecorder listener on the workflow NamedObj. After running tpc09, I change th... Oliver Soong

12:12 PM Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I profiled Kepler comparing an execution and an execution followed by a parameter change. First, I loaded tpc09 into... Oliver Soong

07:13 PM Bug #4766: Semantic Annotation Editor doesn't close when you click the close button on mac

fixed in r23062 Derik Barseghian

04:40 PM Bug #4791: Actor names no longer have spaces

I'm guessing this is related to the changes to the library/database. Aaron do you know? Derik Barseghian

02:48 PM Bug #4791 (Resolved): Actor names no longer have spaces

At some point the spaces in component names went away. In 1.0 it was e.g. String Constant, but now it's StringConstan... Derik Barseghian

04:33 PM Bug #4458: test for moving kepler directory

Retargeting to post 2.0. Derik Barseghian

04:32 PM Bug #4577: integrate, and separate from save/export, the code for Uploading

This bug is a more of request for refactoring and an RFE (when a remote repository is check-marked, don't always prom... Derik Barseghian

02:43 PM Bug #4790 (Resolved): cmd-click in wrp does not create relation

On a mac, doing a cmd-click in the canvas creates a relation (diamond icon) both in the kepler suite, and kepler 1.0,... Daniel Crawl

02:11 PM Bug #4702: KAR to module conversion utility

Aaron,
This is an inappropriate conversation for this forum. This issue has already been decided. You have already h... David Welker

12:52 PM Bug #4702: KAR to module conversion utility

Thanks David, I agree that it is a non-trivial problem. One that we shouldn't have tried to tackle ourselves. Best ... Aaron Aaron

11:17 AM Bug #4702: KAR to module conversion utility

Aaron,
I don't believe that this is the proper forum for you to air your opinions about the desirability of options ... David Welker

10:53 AM Bug #4702: KAR to module conversion utility

David, thank you for explaining to us why having a centralized modules.txt that contains prioritized dependencies is ... Aaron Aaron

04:13 AM Bug #4702: KAR to module conversion utility

I should point out that there is a less ambitious interpretation of this feature request. And that is, not that we ar... David Welker

04:00 AM Bug #4702: KAR to module conversion utility

Do any actual kar files from 1.0 actually contain jars? If so, is the number sufficient to justify building a utility... David Welker

01:59 PM Bug #4785: move cache object from 1.0 to 2.0

I've been looking at this all morning and I think we should punt on this until after 2.0. We basically need to use t... Chad Berkley

01:49 PM Bug #4580: Error saving/opening KAR that has a workflow with a PortParameter

fixed. Daniel Crawl

12:25 PM Bug #4578: tracking bug for changes to .kepler

changed to always use cache-2.0.0 in r23059. Derik Barseghian

11:01 AM Bug #4789 (Resolved): multiport input to composite actor seems to only pass first token

See attached workflow. The problem is not likely to sit with RExpression itself, as I can move the RExpression actor... Oliver Soong

05:22 AM Bug #4281: ant update produces message about running svn cleanup

Christopher,
I was wondering if you could reproduce this problem still. I just tried to reproduce it using your comm... David Welker

05:07 AM Bug #4328: change-to command checks out across branches

What is the purpose of the -Dbranch option? All branches should be named differently, so this option should not be ne... David Welker

04:31 AM Bug #4311: Build system appears to lock if there is a conflict upon update

This was fixed by Chad in an even better way by taking advantage of command-line options that exist in the svn update... David Welker

04:27 AM Bug #4730: Kepler cannot run workflows stored in KAR files from the command-line.

This bug does not exist when running ant "run-workflow" against an ordinary workflow which is stored in an XML file. ... David Welker

02/10/2010

05:34 PM Bug #4784: Remove or fix and re-enable the fullscreen zoom button

fixed for modules that use tagging in r23056. Derik Barseghian

09:39 AM Bug #4784: Remove or fix and re-enable the fullscreen zoom button

Lets remove it for 2.0. Assigning to Debi. Chad Berkley

05:04 PM Bug #4786 (Resolved): workflow file saved in KAR does not open when extracted

If I save a workflow as a KAR, unjar the KAR, and try to open the workflow xml file, it opens as a text file instead ... Daniel Crawl

03:38 PM Bug #4578: tracking bug for changes to .kepler

After talking w/ Chad and Matt the plan is to mostly leave things as they are. We just need to add version info to so... Derik Barseghian

03:13 PM Bug #4785 (New): move cache object from 1.0 to 2.0

Cache kar objects from 1.0 that contain customized actors (i.e. not those shipped with 1.0) need to be migrated to th... Chad Berkley

03:11 PM Bug #4740: Create Ontology_Catalog sql table in the CORE persistent database

push to 2.X.Y Aaron Aaron

02:50 PM Bug #4723: workflows directory should be moved

kar files are now placed into the persistent data directory at
~/KeplerData/modules/<modulename>/kar
You will need t... Aaron Aaron

11:03 AM Bug #4723: workflows directory should be moved

Workflows directory has been moved into the persistent KeplerData directory. I will also move the module kar directo... Aaron Aaron

09:43 AM Bug #4723: workflows directory should be moved

reassigning to aaron. Chad Berkley

01:18 PM Bug #4580: Error saving/opening KAR that has a workflow with a PortParameter

Reassign to Dan, he's looking at this Derik Barseghian

10:46 AM Bug #4702: KAR to module conversion utility

This bug is for backwards compatibility. Since 2.0 kars do not allow for java classes or jars this utility would all... Aaron Aaron

09:42 AM Bug #4702: KAR to module conversion utility

What was the reason for needing this again? Do we need this for 2.0? Chad Berkley

10:12 AM Bug #4662: roll revision vs. new object ID

At 23040, the revision buttons no longer seem to exist, so I guess these exact symptoms will no longer occur. I'm no... Oliver Soong

10:02 AM Bug #4710: RExpression fails to convert arrayType(niltype)

I think we fixed this in 22692. Oliver Soong

02/09/2010

04:30 PM Bug #4784 (Resolved): Remove or fix and re-enable the fullscreen zoom button

The full-screen button is still in the toolbar and set to do nothing (http://bugzilla.ecoinformatics.org/show_bug.cgi... Derik Barseghian

04:19 PM Bug #3172: windows mouse wheel doesn't scroll canvas

Retargeting this bug to 2.X.Y.
Some related scrolling issues were brought up by Peter during yesterday's REAP call:
... Derik Barseghian

03:56 PM Bug #4783 (New): Standardize workflow parsing to get parameters

There are a few different approaches (SciencePipes, CAMERA, UCGrid, Hydrant, etc.) to get workflow parameters from an... Ilkay Altintas

03:41 PM Bug #4462: Component search in remote repositories not working

then there's a sample of this "kar metadata" file that aaron uploaded here:
http://kepler-dev.nceas.ucsb.edu/kepler/m... ben leinfelder

03:36 PM Bug #4462: Component search in remote repositories not working

if you go on Keper-dev's "dev skin" and search using this squery, you can see the "kar" metadata is returned.
(URL: h... ben leinfelder

03:34 PM Bug #4462: Component search in remote repositories not working

Need to verify with Aaron, but I believe:
components are now being uploaded using a new XML metadata format (a wrappe... ben leinfelder

03:25 PM Bug #2493: actor repository tracking bug

adding dependencies... ben leinfelder

03:04 PM Bug #4781: Use the KarXmlGenerator to create the xml metadata sent to the metacat server during "Upload To Repository" action

KAR Uploads from Kepler now use the new KarXml format. Aaron Aaron

02:01 PM Bug #4697: Semantic Annotation does not increment LSID revision

fixed in r23035 Derik Barseghian

01:55 PM Bug #4782: configuration files do not load with non en_US locale

fixed in r23033. Thanks Chad! Daniel Crawl

12:06 PM Bug #4782: configuration files do not load with non en_US locale

added a method to use a default locale tagged file if the currently set locale is not available. Chad Berkley

11:00 AM Bug #4782 (Resolved): configuration files do not load with non en_US locale

If the locale is not set to en_US, the configuration files do not load. I can reproduce this on my mac by:
export ... Daniel Crawl

11:11 AM Bug #4373: Copyright Statements are Inconsistent

added a flag to update the copyrights for tests. all tests are now updated. Chad Berkley

10:48 AM Bug #4373: Copyright Statements are Inconsistent

The sources in tests/src/ have old and inconsistent copyrights. Daniel Crawl

02/08/2010

06:00 PM Bug #4781 (Resolved): Use the KarXmlGenerator to create the xml metadata sent to the metacat server during "Upload To Repository" action

Use the KarXmlGenerator class to create the xml metadata sent to the metacat server during "Upload To Repository" action Aaron Aaron

05:57 PM Bug #4704: Generate XML for a KARFile

I created one junit test that reads in a test kar file (that I put in the same directory as the Junit test, I guess t... Aaron Aaron

03:51 PM Bug #4773 (New): Data processing on the GPP

Do we allow data processing on the GPP unit? Could it be a Kepler workflow, e.g., for quick QA?QC. Ilkay Altintas

03:49 PM Bug #4762: create gui to control sensor from kepler

How does an issued command go from Kepler to sensor? A sequence diagram showing all the components would be good to e... Ilkay Altintas

03:45 PM Bug #4756: allow saving of sensor workflow output

This could be separated into two different bugs: (a) for writing to Metacat and
(b) for writing to DataTurbine Ilkay Altintas

03:44 PM Bug #4756: allow saving of sensor workflow output

This could be separated into two different bugs: (a) for writing to Metacat and one for writing to DataTurbine Ilkay Altintas

03:42 PM Bug #4755: update workflow run manager and reporting to display runs of sensor workflows

An example report (what comes up when you click on a row for the example site in figure 1) is needed to understand th... Ilkay Altintas

03:39 PM Bug #4754: update metacat workflow execution scheduler

This bug should include the documentation of how to set up the server, how to configure it, etc. Ilkay Altintas

03:34 PM Bug #4753: create gui for scheduled execution of sensor workflows on server

This should have an option to run a workflow continuously.
Another idea is, can we change the frequency of a workflo... Ilkay Altintas

03:30 PM Bug #4752: create a sensor plots gui

What other visualization of data can we come up with in addition to plotting? Ilkay Altintas

03:28 PM Bug #4751: implement "run" for site layout

What director will be used to run the layout? Ilkay Altintas

03:23 PM Bug #4748: create google earth kml from component coordinates

Any other mapping interface? Ilkay Altintas

03:17 PM Bug #4745: load & save site layout to metacat

Another way of doing site documentation(Figure 1 in https://kepler-project.org/developers/incubation/kepler-engineeri... Ilkay Altintas

03:11 PM Bug #4743: create gui to edit documentation metadata for component

Do we know if there's missing information? Are there optional fields and how do they effect the design? Ilkay Altintas

03:08 PM Bug #4742: create engineering view model type

As a start:
1. Does an engineering workflow only produce commands to control, etc. the sensors? Using what actor and ... Ilkay Altintas

03:06 PM Bug #4742: create engineering view model type

We need a definition and distinctionof what scientific workflow vs. engineer workflow is. This could also be thought ... Ilkay Altintas

02:48 PM Bug #4741: create icons for engineering view components

The icons should show explicit input and output ports for easy linking of different entities.
Figure 1 in https://k... Ilkay Altintas

02/06/2010

10:29 AM Bug #4462: Component search in remote repositories not working

In regard to replicating problematic components on Kepler-dev, I sent this email to Sean:
----
If I was correct about... ben leinfelder

10:28 AM Bug #4462: Component search in remote repositories not working

if synchronizing the local repositories is still running the moml parser, then that means you'll be prompted for auth... ben leinfelder

02/05/2010

06:52 PM Bug #4767 (Resolved): error instantiating actor with port types from KAR

Create an Expression actor, give it an input port of type boolean, save it as a KAR into a local repository, then try... Oliver Soong

06:51 PM Bug #4697: Semantic Annotation does not increment LSID revision

works for workflow tagging with Tagging UI in r22915.
Still need to updateRevision for semantically annotating ports. Derik Barseghian

06:24 PM Bug #4697: Semantic Annotation does not increment LSID revision

r22914 updates revision for semantic annotation done via Semantic Type Annotation menu. Need to do this in Tagging mo... Derik Barseghian

06:43 PM Bug #4766 (Resolved): Semantic Annotation Editor doesn't close when you click the close button on mac

Clicking the red X close button on a mac isn't working. Derik Barseghian

06:34 PM Bug #4765 (Resolved): semantic annotation doesn't appear until you click on workflow

If you semantically annotate a workflow via Semantic Type Annotation menu, the tag doesn't appear in the tag bar unti... Derik Barseghian

06:19 PM Bug #4764 (New): ProvenanceRecorder.changeExecuted slow after workflow run

If I run any of the tpc workflows (e.g., tpc09), any subsequent changes to Kepler (say changing workflow parameters) ... Oliver Soong

03:24 PM Bug #4578: tracking bug for changes to .kepler

I suggest creating a version specific directory inside .kepler instead of renaming it.
Something like:
.kepler/v/... Christopher Brooks

02:53 PM Bug #4578: tracking bug for changes to .kepler

Yeah the AuthNamespace as Kepler Instance Identifier fell through when we decided to not write anything to the root o... Aaron Aaron

02:29 PM Bug #4578: tracking bug for changes to .kepler

I'm actually not sure that it doesn't. I'll have to check that out. Chad Berkley

02:27 PM Bug #4578: tracking bug for changes to .kepler

I'm ok with that -- I was erroneously thinking the build system deleted all of .kepler with ant clean-cache.(In reply... Derik Barseghian

02:17 PM Bug #4578: tracking bug for changes to .kepler

the upgrade work I did happens in two parts:
First, if DotKeplerManager (DKM) sees the directory signature of a 1.0 ... Chad Berkley

01:58 PM Bug #4578: tracking bug for changes to .kepler

We've now got KeplerData with module dirs for persistent data, and .kepler for temporary data.
Chad recently added ... Derik Barseghian

12:51 PM Bug #4009: kepler 2.0 must provide everything needed for modules

All module support that is going to be included in 2.0 is now working. If more module support is desired in the futu... Chad Berkley

12:50 PM Bug #4373: Copyright Statements are Inconsistent

All copyrights are now the same, except for files that had non-UC copyrights. Chad Berkley

12:49 PM Bug #4665: Add unit tests for kar functionality

I built one junit test for the kar framework. could and should probably build more. The framework is setup now so i... Chad Berkley

12:20 PM Bug #4686: update copyright statements

All copyright statements are now updated. There is a build command 'update-copyrights' to do this now. Chad Berkley

10:57 AM Bug #4763 (New): create gui to access datalogger program

Provide an interface within engineering view to download, view, upload, and install the program running on the datalo... Daniel Crawl

10:55 AM Bug #4762 (Resolved): create gui to control sensor from kepler

Allow the user to turn on or off or change the sampling rate of a sensor from the engineering view. Daniel Crawl

10:54 AM Bug #4761 (Resolved): install and configure SPAN software on gumstix

Install the SPAN software on gumstix computers and configure it to talk to the CR800 datalogger and appropriate sensors. Daniel Crawl

10:53 AM Bug #4760 (Resolved): software to transfer sensor data from SPAN to DT

Create or use existing software to transfer sensor data from SPAN to dataturbine running on gumstix. Daniel Crawl

10:52 AM Bug #4759 (Resolved): install dataturbine on gumstix

Install dataturbine and java on gumstix. Create docs describing process. Daniel Crawl

10:50 AM Bug #4758 (New): search for site components in kepler's data tab

Archive site layouts stored in dataturbine to metacat so that sensor components may be searched from Kepler.
See f... Daniel Crawl

10:48 AM Bug #4757 (Resolved): transfer sensor data from dataturbine to metacat

Periodically archive sensor data on the dataturbine server into metacat. Also verify that archived sensor data can be... Daniel Crawl

10:46 AM Bug #4756 (Resolved): allow saving of sensor workflow output

Sensor workflows that run on the server can convert raw data into derived data; the derived data should be stored bac... Daniel Crawl

10:44 AM Bug #4755 (Resolved): update workflow run manager and reporting to display runs of sensor workflows

Show the current and past runs of sensor workflows executed on the server in the workflow run manager. Additionally, ... Daniel Crawl

10:40 AM Bug #4754 (Resolved): update metacat workflow execution scheduler

Make any changes necessary to the workflow execution scheduler in Metacat to provide the functionality for bug 4753. ... Daniel Crawl

10:39 AM Bug #4753 (Resolved): create gui for scheduled execution of sensor workflows on server

Provide a GUI to specify workflows to periodically run on a server. Configuration parameters include: the workflow xm... Daniel Crawl

10:37 AM Bug #4752 (Resolved): create a sensor plots gui

Display recent data collected by sensors. Select sensors to display, possibly group by sensor type, different sensors... Daniel Crawl

10:35 AM Bug #4751 (Resolved): implement "run" for site layout

Pressing the run button in the engineering view should show the status of the sensors by changing the color of the... Daniel Crawl

10:34 AM Bug #4750 (New): create wiring table gui

Create a wiring table interface that can describe all the connections between sensors and datalogger(s) at a sensor d... Daniel Crawl

10:32 AM Bug #4749 (New): run google earth within kepler gui

View KML created by bug 4748 within the Kepler GUI (i.e. run GE embedded within Kepler). Daniel Crawl

10:31 AM Bug #4748 (Resolved): create google earth kml from component coordinates

Metadata for components such as sensors can include their location lat/lon/alt. Export coordinates from an engineerin... Daniel Crawl

10:30 AM Bug #4747 (New): import & export site layout to SensorML

Import & export engineering view site to SensorML. Daniel Crawl

10:28 AM Bug #4746 (In Progress): ability to create a Site Layout report

Save all the information in an engineering view site as single, printable document. Daniel Crawl

10:27 AM Bug #4745 (Resolved): load & save site layout to metacat

Load and save a site deployment (including wiring, sensor workflows, etc.) to a dataturbine server. Daniel Crawl

10:26 AM Bug #4744 (Resolved): load & save site layout to local kar file

Load and save a site deployment (including wiring, sensor workflows, etc.) to a KAR file. Daniel Crawl

10:24 AM Bug #4743 (Resolved): create gui to edit documentation metadata for component

Create an interface that allows the user to document various metadata for components at a site, e.g. lat/lon/alt, typ... Daniel Crawl

10:22 AM Bug #4742 (Resolved): create engineering view model type

The engineering view is a separate tool from the normal workflow editor. Add the engineering view to File -> New subm... Daniel Crawl

10:18 AM Bug #4741 (New): create icons for engineering view components

Create icons for engineering view components in Kepler. This includes: sensor, datalogger, dataturbine, etc. Also, ne... Daniel Crawl

09:11 AM Bug #4462: Component search in remote repositories not working

I think the local repositories might still be running the MOML parser. At the very least, they seem to be downloadin... Oliver Soong

09:00 AM Bug #4462: Component search in remote repositories not working

kepler-dev has been wiped clean.
This means we shouldn't be at risk of hosing up the KNB server when issuing searches... ben leinfelder

02/04/2010

09:15 PM Bug #4740: Create Ontology_Catalog sql table in the CORE persistent database

I think the work Sean Riddle has done in the tagging module could help with this since he developed a gui to dynamica... Shawn Bowers

08:56 PM Bug #4740 (New): Create Ontology_Catalog sql table in the CORE persistent database

I ran into our old friend, the "Cannot Find Ontology" error. After much time trying to debug through the OntologyCon... Aaron Aaron

03:54 PM Bug #4731: Documentation Customize on directors and parameters gives ClassCastException

I've changed KeplerDocApplicationSpecializer to ignore dealing with ports on non-entities. This seems to do the trick. Aaron Aaron

08:59 AM Bug #4731: Documentation Customize on directors and parameters gives ClassCastException

This problem occurs in Kepler, but not in Vergil.
The stack trace indicates the problem is in KeplerDocApplicationSp... Christopher Brooks

12:07 AM Bug #4731: Documentation Customize on directors and parameters gives ClassCastException

Thanks Derik I'll look into it. Aaron Aaron

02:28 PM Bug #4736 (New): RFE speed up Suggest Similar Components feature

The Suggest Similar Components feature should be sped up.
E.g. right click on a Display actor and Suggest => Simi... Derik Barseghian

02:25 PM Bug #4503: Suggest Similar Components gives an error

fixed in r22883
this had changed to a ClassCastException when trying to do a "Suggest..." within the wrp suite which... Derik Barseghian

01:59 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

Closing, have tested and seems to be working well. Let me know if you see anything you consider weird with workflow L... Derik Barseghian

01:07 PM Bug #4666: identify problems with converting .kepler-1.0 to .kepler-2.0

I have not found any feasible way to transfer the old cache data out of the 1.0 cache into the 2.0 cache. The differ... Chad Berkley

01:05 PM Bug #4722: find 1.0 -> 2.0 .kepler incompatibilities

The only incompatibilities I've found are in the cached serialized files. I've dealt with this by having the DotKepl... Chad Berkley

12:59 PM Bug #3898: update .kepler instead of removing it between versions

Matt identified these three milestones to be able to close this bug. I believe they are all now met. See my comment... Chad Berkley

12:49 PM Bug #4161: Develop kepler workflow execution engine

Need to move the authentication credentials from the old config system (ptolemy-based) to the new configuration.xml s... ben leinfelder

12:48 PM Bug #4735 (New): Allow params to be passed to ConfigurationManager from the command line

Need a mechanism for passing params to CM from the command line. This is a post 2.0 feature. Chad Berkley

12:43 PM Bug #4734: ant run-workflow-no-gui cannot read configuration

Removed kar entry handlers from the wrp ptolemy config file. actually just removed the whole file since it was total... Chad Berkley

10:47 AM Bug #4734 (Resolved): ant run-workflow-no-gui cannot read configuration

Trying to run a workflow (xml or kar) from the ant task or the kepler.sh script results in an exception reading the s... ben leinfelder

10:39 AM Bug #4730: Kepler cannot run workflows stored in KAR files from the command-line.

This is not just files with spaces in the path - I'm getting an error as well:
Unsupported file type or connection n... ben leinfelder

02/03/2010

10:47 PM Bug #4731 (Resolved): Documentation Customize on directors and parameters gives ClassCastException

If you right click Documentation => Customize on a director or parameter you get a ClassCastException. Derik Barseghian

10:33 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

should be fixed in r22873, but needs testing (notably have not yet tested the various user cancel scenarios). Hopeful... Derik Barseghian

04:22 PM Bug #4666: identify problems with converting .kepler-1.0 to .kepler-2.0

I added code to DotKeplerManager to identify a .kepler version 1.0 directory. If it finds this, it will change the c... Chad Berkley

04:12 PM Bug #4714: Adding actor documentation does not increment LSID

Well the solution I came up with is not ideal, but it works. The KeplerDocumentationAttribute now generates one gene... Aaron Aaron

02:02 PM Bug #4714: Adding actor documentation does not increment LSID

I don't know how to fix this since KeplerDocumentationAttribute is in the ptolemy module. Aaron Aaron

03:44 PM Bug #4730 (Resolved): Kepler cannot run workflows stored in KAR files from the command-line.

If I run:
C:\kepler\build-area>ant run-workflow -Dworkflow="C:\Users\visitor\Desktop\kruger workflows\tpc01-buffalo... Oliver Soong

12:04 PM Bug #4722: find 1.0 -> 2.0 .kepler incompatibilities

I went through all of the standard kar files that shipped with 1.0. None of them have jar or class files embedded in... Chad Berkley

11:48 AM Bug #4595: ViewPane selection does not work with toolbar tear-off

Fixed in r22857. Daniel Crawl

11:41 AM Bug #4723: workflows directory should be moved

If it's meant to be changed by the user at runtime, then yes, it should be moved. Chad Berkley

02/02/2010

05:52 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

issue in comment 5 now fixed.
remaining problem: Save As xml rename event sends the old name through, so provenance ... Derik Barseghian

05:13 PM Bug #4727: Cannot compile Ptolemy from IntelliJ

I've fixed the compilation problem for the time being, but it will crop up again when items are added or removed from... Sean Riddle

04:57 PM Bug #4727 (Resolved): Cannot compile Ptolemy from IntelliJ

I can't compile the ptolemy module from within IntelliJ because the appropriate exclusions and inclusions for ptolemy... Sean Riddle

04:42 PM Bug #4322: Attempting to save changes to a workflow saved in a KAR file fails

User is now queried to save a KAR file instead of xml file. Aaron Aaron

02:49 PM Bug #4723: workflows directory should be moved

Should this also apply to the module kar directories?
e.g.
<keplerRoot>/provenance/kar
moves to
~/KeplerData/module... Aaron Aaron

10:16 AM Bug #4723 (Resolved): workflows directory should be moved

There is a directory 'workflows' in the kepler installation directory where you can save kars and have them automatic... Chad Berkley

10:08 AM Bug #4722 (Resolved): find 1.0 -> 2.0 .kepler incompatibilities

Need to go through the 1.0 .kepler directory and find any kars that have jars/classes and figure out a way to migrate... Chad Berkley

02/01/2010

06:24 PM Bug #4697: Semantic Annotation does not increment LSID revision

Also, if you save a workflow, then semantically annotate it, then close the workflow, you're not prompted to save cha... Derik Barseghian

05:44 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

discussed a bit w/ Aaron, Dan and Ben. It seems like a compromise is to assign a new lsid to a workflow when it's ren... Derik Barseghian

04:10 PM Bug #4721 (Resolved): wrm gets exception when provenance turned off

If provenance is turned off, the workflow run manager gets an exception when running a workflow. Daniel Crawl

02:23 PM Bug #4369: Folder creation when saving a KAR

I can't reproduce this now, something likely got fixed along the way that also fixed whatever stacktrace I was seeing... Aaron Aaron

01/31/2010

09:28 PM Bug #4712: Running Kepler from IntelliJ IDEA does not work

Fixed. David Welker

01/30/2010

12:30 AM Bug #4715: Eclipse metadata in webservice module breaks eclipse project import

The webservice module is a special module which has a web service and its client code to execute kepler workflows. Th... jianwu jianwu

01/29/2010

05:29 PM Bug #4715 (Resolved): Eclipse metadata in webservice module breaks eclipse project import

The webservice module in SVN has eclipse .project and .classpath metadata files that do not get overwritten by runnin... Ayla Khan

04:35 PM Bug #4462: Component search in remote repositories not working

looks like each and every search result is being fully parsed, which then kicks off the data download for EML actors ... ben leinfelder

11:24 AM Bug #4462: Component search in remote repositories not working

Trying to search the kepler dev repository yielded the following errors:
[run] trying to clone tpc02-water-flo... Sean Riddle

04:18 PM Bug #4713: Eclipse build still broken

Dan's change that I committed in in r22681 should fix the eclipse build, it's worked for Dan, Ben and I. Derik Barseghian

11:23 AM Bug #4713 (Resolved): Eclipse build still broken

As mentioned on #kepler yesterday, the eclipse build is broken.
I get 20 Java Build Path Problems about project pt... Derik Barseghian

03:34 PM Bug #4701: Persistent Database needed in Core Module for LSID generation to prevent namespace updating on clean-cache

Done: the table is now in the persistent area for the core module. The connection parameters are in core's configurat... Daniel Crawl

12:25 PM Bug #4714 (Resolved): Adding actor documentation does not increment LSID

Adding documentation to an actor (through [actor context menu]->Documentation->Customize) does not increment the LSID. Sean Riddle

11:23 AM Bug #4712: Running Kepler from IntelliJ IDEA does not work

Running "ant eclipse" and then following the instructions at
https://kepler-project.org/developers/reference/kepler-a... Christopher Brooks

10:25 AM Bug #4712 (Resolved): Running Kepler from IntelliJ IDEA does not work

This is related to the fix for bugs 4705 and 4709 (the change to the way the ptolemy module is checked out and manage... Sean Riddle

08:41 AM Bug #4711 (Resolved): Problem with L.H. actor tree: ActorName,kar

In a clean checkout under Windows, I'm now seeing the
kar files listed in the left hand actor tree.
I see
-Actor... Christopher Brooks

01/28/2010

06:09 PM Bug #4710 (Resolved): RExpression fails to convert arrayType(niltype)

Create a workflow with 2 RExpressions. The first should output c(NA, NA). The second should take the output from th... Oliver Soong

05:49 PM Bug #4709 (Resolved): error updating ptolemy/src

Mark was trying the latest Kepler and ran into a problem with the build system. I believe he did a full checkout of ... Oliver Soong

05:45 PM Bug #4705: ant change-to -Dsuite=wrp gives error

This is fixed. Oliver Soong

01:16 PM Bug #4705: ant change-to -Dsuite=wrp gives error

This has to do with the changes to the ptolemy module that David made last night. He is working on a resolution. Chad Berkley

11:15 AM Bug #4705: ant change-to -Dsuite=wrp gives error

I get this as well with "change-to -Dsuite=kepler" at r22632. Sean Riddle

10:23 AM Bug #4705: ant change-to -Dsuite=wrp gives error

Oh, this is at r22632. Oliver Soong

10:00 AM Bug #4705 (Resolved): ant change-to -Dsuite=wrp gives error

Error: ptolemy is either not a suite or wasn't downloaded correctly.
ptolemy looks like it downloaded, svn returne... Oliver Soong

12:45 PM Bug #4322: Attempting to save changes to a workflow saved in a KAR file fails

Yeah, this still needs to get done. Will make sure to get it into the RC1 release. Aaron Aaron

12:42 PM Bug #4515: Finish and Document the Save/Open KAR file functionality

I think we can close this one now. All core save/open kar functionality has been completed. If we need better docum... Aaron Aaron

12:28 PM Bug #4483: Module dependencies in MoML files

Chad I've added code to ImportModuleDependenciesAction that rebuilds the library after new modules are downloaded. T... Aaron Aaron

10:50 AM Bug #4634: run archive causes NPE when building local repository

This got fixed somewhere along the line. Oliver Soong

10:49 AM Bug #4706 (New): support provenance in master-slave 2.0

provenance should be supported in Master-Slave 2.0. There should be an option on whether to firstly save provenance i... jianwu jianwu

10:38 AM Bug #4559: local repositories not showing up in components tree

Not sure when the last bit got fixed, but it seems to be working now. Oliver Soong

10:19 AM Bug #4682: losing reports from KARs

needed to ensure we were listening to all revisions of the named object.
reopen if the problem persists ben leinfelder

10:07 AM Bug #3072: Security issues with distributed execution

It can be configured by permission policy file at slave side. Users who start slave will know their requirements and ... jianwu jianwu

09:58 AM Bug #3069: start slave from gui

slave should be started in both GUI and command line way. Users may remotely login slave machine, start slave by comm... jianwu jianwu

09:51 AM Bug #3068: rmiregistry should be started programmatically

Users may start Kepler GUI at slave side. They also may only need to start slaveController especially when they can o... jianwu jianwu

01/27/2010

09:41 PM Bug #4682: losing reports from KARs

when I reopen the saved KAR I see that the model (TypedCompositeActor) NamedObj that issues the updateRevision() is a... ben leinfelder

07:49 PM Bug #4682: losing reports from KARs

i'm testing a Map-based ObjectManager implementation so that we don't end up with different namedObjs with the same L... ben leinfelder

03:24 PM Bug #4682: losing reports from KARs

Technically, I think the bug is fixed as of r22615. However, the fix only addresses the swapping reports half of the... Oliver Soong

12:32 PM Bug #4682: losing reports from KARs

I'm not seeing it called for any workflow that i open via a KAR.
It is called when I open a MOML xml file.
Something... ben leinfelder

11:46 AM Bug #4682: losing reports from KARs

I'm finally able to reproduce the bug. It requires a KAR file with a report that has a local LSID (i.e., the workflo... Oliver Soong

09:05 PM Bug #4662: roll revision vs. new object ID

This sounds like a WRP specific issue. Reassigning to Ben for the meantime.
Oliver the short answer to having Objec... Aaron Aaron

08:54 PM Bug #4559: local repositories not showing up in components tree

Oliver, can you recheck if this is still happening and close this bug if it is covered in other bugs or succinctly st... Aaron Aaron

08:42 PM Bug #4704: Generate XML for a KARFile

Shell code has been created in the core module: org.kepler.kar.karxml.KarXmlGenerator Aaron Aaron

08:42 PM Bug #4704 (Resolved): Generate XML for a KARFile

Create an XML string based on the Manifest and Entries of a KARFile.
See the example karxml file at the bottom of
... Aaron Aaron

06:02 PM Bug #4701: Persistent Database needed in Core Module for LSID generation to prevent namespace updating on clean-cache

Of those two options, I definitely vote for a 3rd database. One of the main reasons for the DB overhaul was to suppor... Derik Barseghian

04:53 PM Bug #4701 (Resolved): Persistent Database needed in Core Module for LSID generation to prevent namespace updating on clean-cache

The need to use a database table to generate new LSID revisions (ref bug 4633) spawned a new database table called LS... Aaron Aaron

05:13 PM Bug #4463: Grey out component names in the component library that can not be dragged to the canvas

It is unlikely we will need/want to do this in the future. Closing this bug. Aaron Aaron

05:07 PM Bug #4317: KAR's dependencies on modules need to be included in KAR metadata

A KAR's module dependencies are now included in the KAR manifest file and are accessible through the KARFile class. Aaron Aaron

05:04 PM Bug #1750: Allow KAR files to include jar/class files

It was agreed that the solution to this is to create a java utility for converting KAR files to Kepler modules. See ... Aaron Aaron

05:03 PM Bug #4702 (Resolved): KAR to module conversion utility

Create a utility that converts KAR files (version 1.0 and 2.0) to Kepler modules.
This was previously bug 1750. Aaron Aaron

04:54 PM Bug #4633: LSID conflicts

Closing this bug. Opening a new bug (bug 4701) with the one remaining task of moving the LSID_GENERATOR table. Aaron Aaron

04:21 PM Bug #4538: problems with KARs that contain tags from default ontologies

Seems like this got fixed a while back. Closing unless there are any objections. Sean Riddle

02:40 PM Bug #4700 (In Progress): Reminder Update Wiki information to reflect Kepler 2.0 release.

Update the information on the Wiki to include changes to Kepler in the 2.0 release. Remove any information in the Wik... debi staggs

02:39 PM Bug #4699 (In Progress): Reminder Bug Update FAQ to reflect Kepler 2.0 release

Update the FAQ with the 2.0 release features. Remove any statements in the FAQ that are outdated or no longer accurate. debi staggs

02:35 PM Bug #4458: test for moving kepler directory

Changing this to an enhancement request since this bug is for creating a test. Derik Barseghian

11:49 AM Bug #4697: Semantic Annotation does not increment LSID revision

This is more general. Semantically annotating a workflow does not increment the workflow's lsid revision. Derik Barseghian

11:28 AM Bug #4304: Progress monitor is blank when authenticating for KAR upload

Progress monitor has been replaced with a change in the mouse cursor to indicate that authentication is occurring. Sean Riddle

01/26/2010

07:46 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

bug in comment 1 is sort of fixed with r22611. Rename from canvas context menu will work (provenance will rename past... Derik Barseghian

06:46 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

Additional similar bug#2: if you Save Archive, rename, cancel on the save to kar, the workflow and title are renamed,... Derik Barseghian

06:10 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

original bug fixed in r22610.
additional bug described in comment 1 not yet fixed. Derik Barseghian

05:16 PM Bug #4696: Title bar doesn't refresh after rename during Save Archive

Also when you use the new Rename context menu item on the canvas, the listeners aren't notified, so the title bar ref... Derik Barseghian

04:33 PM Bug #4696 (Resolved): Title bar doesn't refresh after rename during Save Archive

If you File => Save Archive, rename your Untitled workflow, and then cancel on the save to kar dialog, the workflow's... Derik Barseghian

05:37 PM Bug #4194: Kepler should have the Continous and Modal domains

Done! The Continuous actors are available. It is possible to create
a Modal model.
See
https://kepler-project.org... Christopher Brooks

05:30 PM Bug #4697 (Resolved): Semantic Annotation does not increment LSID revision

If user gives a semantic annotation during Save Archive in ExportArchiveAction (see FIXME), I notice the LSID doesn't... Derik Barseghian

05:21 PM Bug #4673: past runs with workflows that get renamed don't reflect this

Fixed in r22607 Derik Barseghian

02:52 AM Bug #4630: creating and changing relations don't trigger LSID bump

Workflow LSID revision is now being updated when creating, editing, deleting, or moving relations. It is somewhat no... Aaron Aaron

01/25/2010

04:57 PM Bug #4304: Progress monitor is blank when authenticating for KAR upload

I don't think we will have this progress monitor anymore. The new solution is to use the wait cursor instead which i... Aaron Aaron

04:45 PM Bug #4570: dangling file handle for KARs

Fixed now, just needed to call the close() method on the KARFile after opening it. Aaron Aaron

02:38 PM Bug #4010: RExpression2 - tracking for backwards compatibility

Stupid Responses (SRs):
SR1 - you can change the "environment.txt" file in the r module to reflect the correct R_HOME... ben leinfelder

02:26 PM Bug #4010: RExpression2 - tracking for backwards compatibility

Ben ... sorry to ask stupid questions (SQs).
SQ1: I just removed R 2.9.0 from my system and now have R 2.10.1. Ho... Tom Parris

11:23 AM Bug #4673: past runs with workflows that get renamed don't reflect this

The reason there's the problem in 2) is that ExportArchiveAction does not notify KeplerGraphFrameSave listeners like ... Derik Barseghian

11:14 AM Bug #4538: problems with KARs that contain tags from default ontologies

Things had changed and the concept_label was no longer in the tags in the workflowRun. Sean added the concept_label b... Derik Barseghian

11:06 AM Bug #4479: Error messages are not imported during run import

This was fixed in r21366. Derik Barseghian

01/24/2010

08:08 PM Bug #4380: Removing LocalRepository does not remove actors from Ontologies

(In reply to comment #2)
> Fixed in rev 22588
*rev 22589 Aaron Aaron

08:07 PM Bug #4380: Removing LocalRepository does not remove actors from Ontologies

Fixed in rev 22588 Aaron Aaron

04:23 PM Bug #4362: component search performance

Since the search has been integrated into the Library Index and the Library no longer uses the ActorMetadata objects ... Aaron Aaron

04:18 PM Bug #4629: Undo doesn't roll LSID revision

Undo and redo actions now roll the revision of the lsid in workflows. As of rev 22588 Aaron Aaron

12:34 PM Bug #4581: Handle multiple revisions of components in the Component Library

This solution is working well now. Closing this bug. Aaron Aaron

01/22/2010

03:30 PM Bug #4694 (Resolved): workflow run manager - differentiate imported runs

Eric requests a way to differentiate imported runs ("husk runs") from those you actually ran. One idea is to change t... Derik Barseghian

11:03 AM Bug #4693 (In Progress): Ability to save just a report instance

Eric requests the ability to easily save just the report instance. This should probably be a 1 step process when you'... Derik Barseghian

01/21/2010

06:21 PM Bug #4682: losing reports from KARs

I lost another report. I started Kepler, loaded a KAR (that I had just been editing before restarting Kepler), added... Oliver Soong

05:10 PM Bug #4671: cannot export workflow runs when workflow has actors with <> in the names

retargeting to wrp - though perhaps it's a larger kepler issue? ben leinfelder

04:29 PM Bug #4673: past runs with workflows that get renamed don't reflect this

Correction to my last comment:
1) provenace renames past runs if you do a Save As.
2) If you do a Save Archive they o... Derik Barseghian

01:59 PM Bug #4689 (Resolved): Export run creates duplicate WorkflowRun files. Exporting it again gives none.

Oliver and I both have this problem after the big KAR change.
Aaron, I think you mentioned being aware of the dupli... Derik Barseghian

12:29 PM Bug #4686 (Resolved): update copyright statements

all files in the src tree need to either have copyrights added or existing copyrights updated before the release. Chad Berkley

12:13 PM Bug #4685 (Resolved): Create installers

Create the installers for the 2.0 release and pre-releases. Chad Berkley

12:04 PM Bug #4684 (Resolved): Release tracking bug

All the stuff to do before the release. One bug per task blocking this one. Chad Berkley