Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-11-10T21:53:05ZEcoinformatics Redmine
Redmine Bug #5237 (Resolved): Downloading kars on os X 10.6 locks Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/52372010-11-10T21:53:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you search for and attempt to download a remote KAR when on a mac with 10.6, Kepler freezes forever. This doesn't happen on 10.5, or other linux or windows.</p> Bug #5225 (Resolved): problems loading & saving KARs when disconnectedhttps://projects.ecoinformatics.org/ecoinfo/issues/52252010-10-26T18:22:05ZDaniel Crawldanielcrawl@gmail.com
<p>I can't open a workflow KAR without a network connection. Here's the exception:</p>
<p>org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:530)<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:242)<br /> at org.kepler.kar.KARFile.open(KARFile.java:968)<br /> at org.kepler.kar.KARFile.openKARContents(KARFile.java:736)<br /> at org.kepler.gui.kar.OpenArchiveAction.openKAR(OpenArchiveAction.java:182)<br /> at org.kepler.gui.kar.OpenArchiveAction.actionPerformed(OpenArchiveAction.java:160)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6348)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> at java.awt.Component.processEvent(Component.java:6113)<br /> at java.awt.Container.processEvent(Container.java:2085)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4714)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2143)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2129)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): ptolemy.eecs.berkeley.edu<br /> at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:260)<br /> at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1792)<br /> at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1751)<br /> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)<br /> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:518)<br /> ... 33 more</p>
<p>I also get the following exception when I save a KAR, but the KAR appears to be created:</p>
<p>done writing KAR file to /Users/crawl/KeplerData/workflows/MyWorkflows/01-SimpleAddition.kar<br />java.net.UnknownHostException: ptolemy.eecs.berkeley.edu<br /> at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)<br /> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:432)<br /> at java.net.Socket.connect(Socket.java:529)<br /> at java.net.Socket.connect(Socket.java:478)<br /> at sun.net.NetworkClient.doConnect(NetworkClient.java:163)<br /> at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)<br /> at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)<br /> at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)<br /> at sun.net.www.http.HttpClient.New(HttpClient.java:306)<br /> at sun.net.www.http.HttpClient.New(HttpClient.java:323)<br /> at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:860)<br /> at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:801)<br /> at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:726)<br /> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1049)<br /> at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)<br /> at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)<br /> at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)<br /> at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)<br /> at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source)<br /> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)<br /> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br /> at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br /> at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)<br /> at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(KeplerMetadataExtractor.java:104)<br /> at org.kepler.objectmanager.cache.ActorCacheObject.<init>(ActorCacheObject.java:143)<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(ActorMetadataKAREntryHandler.java:212)<br /> at org.kepler.kar.KARFile.cache(KARFile.java:920)<br /> at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:633)<br /> at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:185)<br /> at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(ExportArchiveAction.java:429)<br /> at org.kepler.gui.kar.SaveArchiveAction.actionPerformed(SaveArchiveAction.java:89)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6348)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> at java.awt.Component.processEvent(Component.java:6113)<br /> at java.awt.Container.processEvent(Container.java:2085)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4714)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2143)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2129)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Error parsing Actor KAR DOM "<?xml version="1.0"?><br /><!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br /> "http://ptolemy.e...": ptolemy.eecs.berkeley.edu<br />MC 18:57:45,405: [WARN]: KAREntry has no lsid: null [org.kepler.objectmanager.cache.CacheManager]</p> Bug #5161 (Resolved): can't always use Module Manager to change to an older patch of a suitehttps://projects.ecoinformatics.org/ecoinfo/issues/51612010-08-25T23:27:04ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If a module is published<br />and a patched version of this module is published<br />and the user has downloaded both<br />and the user uses the MM to change to the original version of the module<br />Kepler will restart and automatically use the newest patch of the module that's available on the local system, with no notice.</p>
<p>I would expect a user would be able to intentionally change to the old patch, especially since it's visible in the MM's gui.<br />Even if 'Automatically download new patches' is left on, they should get the prompt for an update on restart, I would think.</p>
<p>Is this a known issue, compromise, or intentional choice the MM is currently making? It's not strictly necessary for 2.1, because the Import Module Dependencies feature does allow this (and that's when it's <strong>really</strong> necessary). Also since the IMD feature can prompt a user to do this (restart into an older patch), I think a user would think they could also use the MM to do it.</p> Bug #5157 (Resolved): Devise approach for when patching should occur when changes occur via the m...https://projects.ecoinformatics.org/ecoinfo/issues/51572010-08-20T18:28:39ZDavid Welkerdavid.v.welker@gmail.com
<p>Right now, if you change to a suite through the module manager, it is listed as not being patchable. This might be desirable behavior. Need to devise changes so that patching is possible after changes with the module manager.</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 #5127 (Resolved): Make a good way to publish a suite without changing a bunch of modules.txt ...https://projects.ecoinformatics.org/ecoinfo/issues/51272010-08-04T19:34:22ZSean Riddleswriddle@gmail.com
<p>As shown in the publishing instructions page on the wiki (<a class="external" href="https://kepler-project.org/developers/teams/build/documentation/publishing-steps/">https://kepler-project.org/developers/teams/build/documentation/publishing-steps/</a>), you have to manually modify the modules.txt file from each module branch that you are publishing. It would be nice if this process were streamlined.</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 #5101 (Resolved): Composite Actor windows show wrong title after workflow Renamehttps://projects.ecoinformatics.org/ecoinfo/issues/51012010-07-21T20:23:11ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you use the canvas Rename context menu to rename your workflow that contains composite actors, then Open Actor to see a composite actor's contents in a new window, this new window's title bar shows old_workflow_name#CompositeActor instead of new_name#CompositeActor. It doesn't matter if the Composite has been instantiated before or after the rename (so at least it's consistent).</p>
<p>You must currently Save or Save Archive before the composite actor windows use the right name in the title bar.</p> Bug #5098 (Resolved): Save Archive (KAR)... will have exception when internet is not accessible.https://projects.ecoinformatics.org/ecoinfo/issues/50982010-07-19T22:30:21Zjianwu jianwujianwu@sdsc.edu
<p>Found by Chris Weed, I can reproduce it.</p>
<p>It happens when I right-click the actor, choose 'Save Archive (KAR)...' and try to save its kar file, no matter whether I choose 'Add Semantic Types' or not. </p>
<pre><code>[null] done writing KAR file to C:\Users\jianwu\KeplerData\workflows\MyWorkflows\ttt.kar<br /> [null] java.net.UnknownHostException: ptolemy.eecs.berkeley.edu<br /> [null] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)<br /> [null] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)<br /> [null] at java.net.Socket.connect(Socket.java:529)<br /> [null] at java.net.Socket.connect(Socket.java:478)<br /> [null] at sun.net.NetworkClient.doConnect(NetworkClient.java:163)<br /> [null] at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)<br /> [null] at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)<br /> [null] at sun.net.www.http.HttpClient.&lt;init&gt;(HttpClient.java:233)<br /> [null] at sun.net.www.http.HttpClient.New(HttpClient.java:306)<br /> [null] at sun.net.www.http.HttpClient.New(HttpClient.java:323)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:860)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:801)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:726)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1049)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br /> [null] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)<br /> [null] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(KeplerMetadataExtractor.java:101)<br /> [null] at org.kepler.objectmanager.cache.ActorCacheObject.&lt;init&gt;(ActorCacheObject.java:141)<br /> [null] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(ActorMetadataKAREntryHandler.java:169)<br /> [null] at org.kepler.kar.KARFile.cache(KARFile.java:876)<br /> [null] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:591)<br /> [null] at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:184)<br /> [null] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(ExportArchiveAction.java:344)<br /> [null] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)<br /> [null] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)<br /> [null] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> [null] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> [null] at javax.swing.AbstractButton.doClick(AbstractButton.java:357)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> [null] at java.awt.Component.processMouseEvent(Component.java:6263)<br /> [null] at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> [null] at java.awt.Component.processEvent(Component.java:6028)<br /> [null] at java.awt.Container.processEvent(Container.java:2041)<br /> [null] at java.awt.Component.dispatchEventImpl(Component.java:4630)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2099)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [null] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)<br /> [null] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br /> [null] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2085)<br /> [null] at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [null] at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> [null] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br /> [null] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [null] Error parsing Actor KAR DOM "<?xml version="1.0"?><br /> [null] &lt;!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br /> [null] "http://ptolemy.e...": ptolemy.eecs.berkeley.edu<br /> [null] WARN (org.kepler.objectmanager.cache.CacheManager:insertObject:237)<br /> KAREntry has no lsid: null</code></pre>
<pre><code>It has similar exception when proxy is needed to access internet. The problem Chris found is as follows.</code></pre>
<p>I think the problem I am having is that it is trying to validate the XML against<br /><a class="external" href="http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd">http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd</a>, and my proxy<br />is probably in the way. Although I set the proxy in the kepler.bat file on the<br />command-line. I am not sure why it isn't going through.<br />Chris</p>
<p>[null] java.net.ConnectException: Connection timed out: connect<br />[null] at java.net.PlainSocketImpl.socketConnect(Native Method)<br />[null] at java.net.PlainSocketImpl.doConnect(Unknown Source)<br />[null] at java.net.PlainSocketImpl.connectToAddress(Unknown Source)<br />[null] at java.net.PlainSocketImpl.connect(Unknown Source)<br />[null] at java.net.SocksSocketImpl.connect(Unknown Source)<br />[null] at java.net.Socket.connect(Unknown Source)<br />[null] at java.net.Socket.connect(Unknown Source)<br />[null] at sun.net.NetworkClient.doConnect(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.openServer(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.openServer(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.<init>(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.New(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.New(Unknown Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(<br />Unknown Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unkn<br />own Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown S<br />ource)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Un<br />known Source)<br />[null] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Un<br />known Source)<br />[null] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown S<br />ource)<br />[null] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknow<br />n Source)<br />[null] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unkno<br />wn Source)<br />[null] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.d<br />ispatch(Unknown Source)<br />[null] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDoc<br />ument(Unknown Source)<br />[null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So<br />urce)<br />[null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So<br />urce)<br />[null] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br />[null] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br />[null] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Sour<br />ce)<br />[null] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(<br />KeplerMetadataExtractor.java:101)<br />[null] at org.kepler.objectmanager.cache.ActorCacheObject.<init>(ActorC<br />acheObject.java:141)<br />[null] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(Ac<br />torMetadataKAREntryHandler.java:169)<br />[null] at org.kepler.kar.KARFile.cache(KARFile.java:876)<br />[null] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:591)<br />[null] at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:184)<br />[null] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(Export<br />ArchiveAction.java:344)<br />[null] at javax.swing.AbstractButton.fireActionPerformed(Unknown Source<br />)<br />[null] at javax.swing.AbstractButton$Handler.actionPerformed(Unknown So<br />urce)<br />[null] at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown So<br />urce)<br />[null] at javax.swing.DefaultButtonModel.setPressed(Unknown Source)<br />[null] at javax.swing.AbstractButton.doClick(Unknown Source)<br />[null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source<br />)<br />[null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(<br />Unknown Source)<br />[null] at java.awt.Component.processMouseEvent(Unknown Source)<br />[null] at javax.swing.JComponent.processMouseEvent(Unknown Source)<br />[null] at java.awt.Component.processEvent(Unknown Source)<br />[null] at java.awt.Container.processEvent(Unknown Source)<br />[null] at java.awt.Component.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Container.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Component.dispatchEvent(Unknown Source)<br />[null] at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Sou<br />rce)<br />[null] at java.awt.LightweightDispatcher.processMouseEvent(Unknown Sour<br />ce)<br />[null] at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)<br />[null] at java.awt.Container.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Window.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Component.dispatchEvent(Unknown Source)<br />[null] at java.awt.EventQueue.dispatchEvent(Unknown Source)<br />[null] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown S<br />ource)<br />[null] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Sour<br />ce)<br />[null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown S<br />ource)<br />[null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br />[null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br />[null] at java.awt.EventDispatchThread.run(Unknown Source)<br />[null] Error parsing Actor KAR DOM "<?xml version="1.0"?><br />[null] <!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br />[null] "http://ptolemy.e...": Connection timed out: connect<br />[null] WARN (org.kepler.objectmanager.cache.CacheManager:insertObject:237)<br />KAREntry has no lsid: null</p> Bug #5093 (Resolved): module manager can leave kepler in broken or unexpected stateshttps://projects.ecoinformatics.org/ecoinfo/issues/50932010-07-14T17:54:57ZDaniel Crawldanielcrawl@gmail.com
<p>The module manager lets one "change to" individual modules instead of only suites. This can lead to a situation where kepler cannot be started. (This happened to me when I selected only the data-handling-2.0.0 module).</p>
<p>Additionally, more than one suite can be selected at a time. However, it appears that only the first on the list is used. (I selected tagging and reporting, with tagging being first, and ended up with only tagging).</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> Bug #5074 (Resolved): Fix the release process so modules can be released from Windows machines.https://projects.ecoinformatics.org/ecoinfo/issues/50742010-07-01T03:50:00ZDavid Welkerwelker4kepler@gmail.com
<p>(10) Fix the release process so modules can be released from Windows machines.</p>
<p>Currently, the release process often fails when attempted from Windows. This may or may not be fixable; I suspect that this is due to limitations in the SVN client on Windows. However, this problem should be investigated and fixed if possible.</p> Bug #5073 (Resolved): In module manager, display the current suite name as well as a fully resolv...https://projects.ecoinformatics.org/ecoinfo/issues/50732010-07-01T03:49:30ZDavid Welkerwelker4kepler@gmail.com
<p>(9) In module manager, display the current suite name as well as a fully resolved list of modules.</p>
<p>The module manager currently displays the content of modules.txt. If modules.txt refers to other suites, it is not possible to tell what modules are actually in use. Also, it is not possible to tell what the current suite (if it is non-custom) is currently selected. The module manager display would be more useful if it displayed this information.</p> Bug #5070 (Resolved): Changing the "Available Modules" tab in the Module Manager to "Available Su...https://projects.ecoinformatics.org/ecoinfo/issues/50702010-07-01T03:48:18ZDavid Welkerwelker4kepler@gmail.com
<p>(6) Changing the "Available Modules" tab in the Module Manager to "Available Suites and Modules"</p>
<p>This is a minor change that could be made to make the GUI more clear.</p> Bug #5065 (Resolved): In shared or administrative installations, the ability to store modules.txt...https://projects.ecoinformatics.org/ecoinfo/issues/50652010-07-01T03:42:36ZDavid Welkerwelker4kepler@gmail.com
<p>(1) In shared or administrative installations, the ability to store modules.txt and extra modules locally. This way, the module manager will work smoothly on Windows without having to run as an administrator.</p>
<p>Problem: The file modules.txt is read by Kepler to determine which modules are active. Both modules.txt and local modules are currently stored in the installation area, which in shared installations is read-only. Because extra modules are executed, security might dictate that in shared installation situations modules.txt not be changed and new modules not be downloaded. This was the original rationale for going forward with our current design However, on Windows, the default for installations appears to be to install as an administrator. As a result, even in private non-shared installations on Windows, it can be difficult to use the Module Manager. To do so, a user must remember to run as an administrator, which gives Kepler the ability to write to the installation area.</p>
<p>Solution 1: Store modules.txt and download new modules not to the installation area, but to a designated location in the users home where write access will be available. The downside of this approach is that this would decrease the security of truly shared installations of Kepler. On the other hand, a problem with malicious modules may be more theoretical than real at this point, as modules are now published and retrieved from a centralized source that we control. Also, if there is a problem with malicious modules, it would affect not just shared installations, but individual installations; protecting shared installations does nothing to protect individual installations which are perhaps just as important. Also, the real risk of malicious modules is low, given current development patterns.</p>
<p>Solution 2: Try to find a way so that Windows installations are not done by default on Windows. This may or may not be possible.</p>
<p>Solution 3: Warn users who do not have appropriate write permissions to the installation area that they may not use the Module Manager. The design of such a warning should be thought through so that it is non-intrusive and graceful. For example, it probably should not pop-up at start-up, but only when the user attempts to invoke Module Manager functionality.</p>
<p>Conclusion: At the very least, users who cannot use the Module Manager due to lack of permission to write to where Kepler has been installed should be warned. Perhaps even better, given the prevalence of this problem in Windows and relatively low security risks, modules.txt and new module downloads should occur in a local area that is writable.</p>