Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-03-15T20:56:47ZEcoinformatics Redmine
Redmine Bug #5352 (Resolved): build-area-2.1 is not working and build-area-2.2 is needed for kepler-2.2 r...https://projects.ecoinformatics.org/ecoinfo/issues/53522011-03-15T20:56:47Zjianwu jianwujianwu@sdsc.edu
<p>I didn't see build-area-2.2 module for kepler-2.2 at <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/">https://code.kepler-project.org/code/kepler/releases/release-branches/</a> or <a class="external" href="https://code.kepler-project.org/code/kepler/releases/released/">https://code.kepler-project.org/code/kepler/releases/released/</a>. When I tried to use <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1/">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1/</a>, I got the following exception. Since kepler trunk is ever changing, we'd better have a build-area-2.2 module for kepler 2.2 release.</p>
<p>kepler:build-area-2.1 jianwu$ svn info<br />Path: .<br />URL: <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1</a><br />Repository Root: <a class="external" href="https://code.kepler-project.org/code/kepler">https://code.kepler-project.org/code/kepler</a><br />Repository UUID: edc41a2b-3e5c-0410-9d3f-8540a70682f1<br />Revision: 27291<br />Node Kind: directory<br />Schedule: normal<br />Last Changed Author: welker<br />Last Changed Rev: 26871<br />Last Changed Date: 2011-01-31 14:25:53 -0800 (Mon, 31 Jan 2011)</p>
<p>kepler:build-area-2.1 jianwu$ ant<br />Buildfile: /Users/jianwu/Kepler/repository/kepler/kepler-branch-2.2/build-area-2.1/build.xml</p>
<p>BUILD FAILED<br />/Users/jianwu/Kepler/repository/kepler/kepler-branch-2.2/build-area-2.1/build.xml:4: The following error occurred while executing this line:<br />/Users/jianwu/Kepler/repository/kepler/kepler-branch-2.2/build-area-2.1/settings/taskdefs.xml:5: typedef class org.kepler.build.Get cannot be found<br /> using the classloader AntClassLoader[]</p>
<p>Total time: 0 seconds</p> Bug #5334 (Resolved): 2.2 rc3: kepler.sh file is not executable by default in Kepler.app/Contents...https://projects.ecoinformatics.org/ecoinfo/issues/53342011-03-01T23:52:08Zjianwu jianwujianwu@sdsc.edu
<p>I think many users need to use kepler.sh or kepler.bat to get console information. But in my installation on mac, Kepler.app/Contents/Resources/Java/kepler.sh is not executable. I have to change mode to run it.</p> Bug #5328 (Resolved): 2.2rc2 - standalone module manager won't starthttps://projects.ecoinformatics.org/ecoinfo/issues/53282011-02-26T01:40:00ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>On mac 10.6 and windows XP, both with java 1.6, I can't get the standalone module manager application to start. On windows I tried both shortcuts and the executable itself. I didn't have this problem in the last rc.</p> Bug #5326 (Resolved): 2.2rc2 - upgrade config file bug workaround moves KeplerData/modules to Kep...https://projects.ecoinformatics.org/ecoinfo/issues/53262011-02-25T22:03:56ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The workflow-around for the configuration file bug is to move a user's existing KeplerData/modules to KeplerData/modules.old during the first launch of 2.2. However I think we should instead just do something along the lines of moving each module's configuration dir to a configuration.old. The issue is that more than just config files reside in KeplerData/modules. E.g. the coreDB and provenance databases.</p> Bug #5325 (Resolved): 2.2rc2 - documentation problemshttps://projects.ecoinformatics.org/ecoinfo/issues/53252011-02-25T21:26:09ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>1) Most links in the pdfs don't work - you just see blue text.</p>
<p>2) User Manual Section 6 doesn't include changes to 6.0WorkingWithDatasets.doc. My guess is you didn't build the user manual from the individual chapters but instead edited a copy of the 2.1.0 version (?). If you're taking that route, you'll have to be careful with keeping TOC in sync and include changes from other files more recent than 2.1.0 docs:</p>
<p><del>rw-r--r-</del> 1 derik derik 28614618 Sep 28 13:13 KeplerUserManual-2.1.0.pdf<br /><del>rw-r--r-</del> 1 derik derik 27385066 Sep 28 13:13 KeplerUserManual-2.1.0.doc<br /><del>rw-r--r-</del>@ 1 derik derik 2173091 Jan 11 13:53 6.0WorkingWithDatasets.doc<br /><del>rw-r--r-</del> 1 derik derik 214528 Jan 19 13:07 A.BModules.doc<br /><del>rw-r--r-</del> 1 derik derik 28160 Feb 22 17:15 Title Page.doc</p>
<p>3) Remote Copy links of Getting Started Guide and Actor Reference link to 1.0.0 versions.</p>
<p>4) Copyright link to copyright.htm is 2003-2010. Should update to 2011.</p> Bug #5318 (Resolved): 2.2.0 release testinghttps://projects.ecoinformatics.org/ecoinfo/issues/53182011-02-23T00:03:50ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>David asked me to create a list of less obvious things to test for 2.2. Obviously this isn't comprehensive; please test other things as you go.</p>
<p>Note: you have to download the installer for 2.2; upgrading to 2.2 via the module manager within 2.1 or 2.0 will not work. Also note the 2.2 installer includes a standalone Module Manager app.</p>
<p>Test Kepler 2.0.0 to 2.2.0 transition:<br />---------------<br />Developers, remove any trunk generated artifacts: rm -rf ~/.keeper ~/KeplerData;<br />Start Kepler-2.0.0 installed on your machine from the 2.0 installer.<br />Components=>Sources=>check-mark the kepler repository as a Search item. This will cause a write of ~/KeplerData/modules/repository/configuration/configuration.xml.<br />Test Components search. Use <a class="external" href="http://kepler-dev.nceas.ucsb.edu/kepler/">http://kepler-dev.nceas.ucsb.edu/kepler/</a> to verify your results.<br />Test Data search. E.g. for aphid. Drag out a data source.<br />Create a simple workflow, e.g. SDF w/ 1 iteration, String Constant=>Display. Execute. Save to kar. Export to xml.<br />Quit 2.0.0. <br />Install 2.2.0 from the 2.2 installer.<br />Launch 2.2.0, click the Sources button. Verify this dialog comes up, and that your old, incompatible config file(s) in KeplerData have been moved out of the way, into a separate directory.<br />Navigate to Sources=>Preferences=>KAR Preferences and select strict.<br />Attempt to open the kar you saved in 2.0.0. Obligue the dialog, restart into 2.0.0.<br />A known limitation is that to return to 2.2.0 you should not use the Module Manager inside Kepler, use the standalone Module Manager application that ships with 2.2.0 to restart into 2.2.0.</p>
<p>Test Kepler 2.1.0 to 2.2.0 transition.<br />--------------------<br />Similar to above, but first upgrade your installed version of 2.0.0 to kepler-2.1.0 and/or reporting-2.1.0 via the 2.0.0 module manager. <br />Create a reporting 2.1.0 kar by exporting a run from the Workflow Run Manager. Attempt to open this kar from 2.2.0 in Strict mode, etc.</p>
Misc 2.2 tests:<br />----------------
<ul>
<li>Test the built in Module Manager.</li>
<li>Test each OS Installer.</li>
<li>Test all outreach demos.</li>
<li>Check Help=>About version number. Check Help=>Kepler Documentation -- test all links.</li>
<li>Create, save, right-click rename on canvas, export, run and open a workflow.</li>
<li>Search the Kepler repository via Components tab.</li>
<li>Search for remote data using Data tab.</li>
<li>Right-click on a kar and upload to the Kepler repository -- ideally the workflow has documentation, serves as a good example, and may be left on the repository for users, otherwise subsequently delete it. Contact myself, jing or ben for help deleting.</li>
<li>Outline tab - drag a workflow component out to canvas. Then delete it.</li>
</ul> Bug #5311 (Resolved): 2.2.0rc1 - remote data sources don't workhttps://projects.ecoinformatics.org/ecoinfo/issues/53112011-02-15T21:56:43ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>In 2.2.0rc1 installed from the installer, remote data sources don't work. <br />I discovered this when trying to open PythonGenericDialog.xml demo workflow.<br />It also happens when you search the Data tab and try to drag out a data source.</p>
<p>The error message you see comes from EcogridDataCacheItem and is:<br />There has been a problem accessing the remote data<br />java.lang.String cannot be cast to [B</p>
<p>This doesn't appear to happen from trunk, or from 2.2.0 launched from the module manager. I'm not clear on why this is...</p> Bug #5310 (Resolved): 2.2.0rc1 - Documentation link problemshttps://projects.ecoinformatics.org/ecoinfo/issues/53102011-02-15T21:36:57ZDerik Barseghianbarseghian@nceas.ucsb.edu
Some issues with Help->Documentation in 2.2.0rc1:
<ul>
<li>None of the Local Copy links to documentation (at Help->Kepler Documentation) work.</li>
<li>The Remote Copy links point to 1.0 docs.</li>
<li>The workflow links don't work</li>
</ul> Bug #5309 (Resolved): 2.2.0rc1 - Preferences and Components Search (configuration) issuehttps://projects.ecoinformatics.org/ecoinfo/issues/53092011-02-15T21:34:41ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I've given the mac installer a try and I've run into the configuration file issue - my ~/KeplerData/repository/configuration/configuration.xml does not contain the new properties authorizationPath or authenticatedquerypath and I get errors as a result. I also don't see old versions of my configuration files -- I believe the workaround that you implemented for <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5129">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5129</a> was that the old configs are supposed to be moved out of the way on the first startup of 2.2.</p>
<p>Here's what I did:<br />cd ~/kepler.modules/build-area/; ant clean-all; rm -rf ~/KeplerData;<br />Start up previously installed Kepler 2.1.0 from Applications<br />Change my Components Sources to search the Kepler repository<br />Change Kar Preferences to Strict<br />Search for sdf. Create and run a simple workflow<br />Quit<br />Start installer 2.2.0rc1 from Applications<br />Clicking on the Sources button gives the below error. Attempting to search Components also gives an error.</p> Bug #5263 (Resolved): failure to restart after upgrade from 2.0 to 2.1https://projects.ecoinformatics.org/ecoinfo/issues/52632010-12-24T01:46:43ZMatt Jonesjones@nceas.ucsb.edu
<p>You are receiving this mail because Pranav Godbole<br /><a class="email" href="mailto:ingi_05@hotmail.com">ingi_05@hotmail.com</a><br />is sending feedback about the site administered by you at <a class="external" href="https://kepler-project.org">https://kepler-project.org</a>.<br />The message sent was:</p>
<p>Hello, I'm having some difficulty updating from 2.0 to 2.1 on Windows 7. After following the steps outlined on the site, the application does not seem to do anything after I click the "apply and restart" button. It seems to stick at 'initializing' and does not restart even after waiting appox. 45min.</p>
<p>The second question I have is how do I graph an equation in this software. I'm new to Kepler and workflow softwares in general. I'm trying to apply this technology to help simulate a basic economy. However, I need to be able to graph a line, and have it follow some rules, here is an example : The user must choose a rule. ex. when y > 100; R1 would state divide by 50, R2 states subtract 98. x=2 (this is given by user) plug into y=2x. ' this compounds, so the result of 2*2 will equal x in the next iteration and 4*2 will equal x in the next etc... y > 100. when true, R1 or R2 will be invoked. The real time output will be graphed in Kepler, but the data at given time intervals<br /> should be written to an Excel or CSV file with a time stamp (seconds from t=0) I've looked meticulously for tutorials for both this software and similar ones with no avail. Any help would be much appreciated. Thank you and happy holidays! Pranav</p> Bug #5190 (Resolved): 6.0WorkingWithDatasets describes OPeNDAP but not DataTurbine actorhttps://projects.ecoinformatics.org/ecoinfo/issues/51902010-09-25T02:07:47ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Chapter 6 describes the OPeNDAP actor, but not the DataTurbine actor. Since both are included modules in the kepler suite, both should be described.</p> Bug #5146 (Resolved): modifying and saving the composite sinewave actor failshttps://projects.ecoinformatics.org/ecoinfo/issues/51462010-08-12T00:53:45ZMatt Jonesjones@nceas.ucsb.edu
<p>Trying to make changes to the Sinewave actor that ships with Kepler and then trying to save that actor as a KAR file fails with an error, and the new copy of the actor in the new KAR file is not saved correctly (the output port is missing and not connected, and there are three new boxes labeled "kepler:frequency", "kepler:phase". and "kepler:output" that were not in the original actor.</p>
<p>To reproduce:</p>
<p>1) Drag sinewave to canvas, select, and open<br />2) Modify the Annotation text to say something different.<br />3) Close the sinewave actor<br />4) An error will pop up, with the text "Save changes to jar:file:/Applications/Kepler-2.0/Kepler.app/Kepler/ptolemy-8.0.0/target/ptolemy-8.0.jar!/ptolemy/actor/lib/Sinewave.xml"</p>
<p>5) Click 'Save', which brings up the file naming dialog, choose a new name for the KAR (Sinewave2.kar), and click 'Save' (you may also get prompted to select a semantic type)<br />6) Locate the new KAR in the components panel and drag the contained actor onto the canvas<br />7a) The actor will be missing an output port<br />7b) Opening the actor will show new boxes that didn't exist before, and the missing output port</p>
<p>Expected behavior:<br />There should be no error associated with saving on top of a jar file (this is a KAR file save). The actor should have an output port connected to the same relation as before, and the square boxes should not exist. The actor copy should be identical to the original on the canvas (except maybe the LSID should have changed).</p>
<p>See attached screenshot showing the misconfigured actor.</p> Bug #5144 (Resolved): renaming an actor does not persist in saved kar fileshttps://projects.ecoinformatics.org/ecoinfo/issues/51442010-08-12T00:27:01ZMatt Jonesjones@nceas.ucsb.edu
<p>When one renames an actor on the canvas, and then selects that actor and chooses 'Save KAR...' in the context menu, a new KAR file is saved, but the actor in that KAR file contains the original name of the actor, rather than the new name.</p>
<p>To reproduce:</p>
<p>1) Drag 'Display' (or any other actor) onto the canvas<br />2) Select the actor, right click, and select 'Customize Name' from the menu<br />3) Change the name to 'MyDisplay' or another name, and click 'Commit'<br />4) Right click on the actor again and select 'Save Archive (KAR)...'<br />5) Type a name for the kar (probably 'MyDisplay.kar') and click 'Save'<br />6a) In the component tab, search for 'Display', and navigate to the newly saved kar file, click on the arrow to expand the KAR contents, which will show the original name of the actor (Display)<br />6b) Drag the new actor to the canvas, which will show the original name of the actor (Display)</p>
<p>Expected behavior:<br />For 6a, and 6b, the name shown should be the new name of the actor (e.g., 'MyDisplay')</p>
<p>This is a synopsis of an issue reported by Chris Weed on kepler-users.</p> Bug #5125 (Resolved): Add feature to do a one-step revert of a botched update from outside of Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/51252010-08-04T19:27:10ZSean Riddleswriddle@gmail.com
<p>If a patch does not work correctly, it is possible that Kepler will fail to restart after the patch's installation. The way to handle this (which will be made simpler in the future) is to run the module manager standalone and use it to restore to a working configuration.</p>
<p>The module manager should have an easy way to rollback the last patch that was applied, returning the user to the working configuration they were just in.</p>
<p>This should probably also disable automatic updates.</p> Bug #5084 (Resolved): Allow test releases in the same location as actual releases.https://projects.ecoinformatics.org/ecoinfo/issues/50842010-07-08T21:26:27ZDavid Welkerwelker4kepler@gmail.com
<p>(13) Allow test releases in the same location as actual releases.</p>
<p>Right now, the Kepler module manager can be configured to look at a test-release location rather than the actual release location. However, this is not necessarily ideal because the resources available in the test-release location may not always be identical to the actual release location, or if it is, this requires maintenance and duplication of resources. A possible solution would be to create a flag of some sort (which might be indicated by the presence of a special file, for example) so that test-modules are not shown in the module manager, unless the user selects an appropriate check box or menu item. In this way, test modules would be guaranteed to have access to the same resources as released modules.</p>