Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-08-05T15:08:21ZEcoinformatics Redmine
Redmine Bug #5453 (Resolved): ant javadoc -Dfull=true failshttps://projects.ecoinformatics.org/ecoinfo/issues/54532011-08-05T15:08:21ZChristopher Brookscxh@eecs.berkeley.edu
<p>Running "ant" says</p>
<blockquote>
<p>javadoc Create javadoc for all the modules in modules.txt. Use -Dfull=true if you want to link your documentation to documentation of Kepler and Ptolemy too.</p>
</blockquote>
<p>However, ant javadoc <del>Dfull=true fails.<br />--start-</del></p>
<p>bash-3.2$ ant javadoc -Dfull=true<br />Buildfile: /Users/cxh/src/kepler/build-area/build.xml</p>
<p>javadoc:</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler/build-area/build.xml:204: src '/Users/cxh/src/kepler/null/lib/jar/kepler-r7920.jar' doesn't exist.</p>
<p>Total time: 0 seconds</p>
<p>--end--</p>
<p>ant javadoc -Dfull=true should be part of the nightly test suite.</p> Bug #5451 (Resolved): Componets ->(right mouse) View Dokumentation causes NameDuplicationExceptionhttps://projects.ecoinformatics.org/ecoinfo/issues/54512011-08-05T14:28:58Zunknown unknownmelchiaros@aol.com
<p>When I try to call "View Documentation" (right mouse click on a component->"View Documetation") and there is already a help window open from another comonent, than Kepler popup an error window and throw a exeption:</p>
<p>[null] ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "DocEffigy" into container named ".configuration.directory.effigy3", which already contains an object with that name.<br /> [null] at ptolemy.kernel.util.NamedList.append(NamedList.java:133)<br /> [null] at ptolemy.kernel.CompositeEntity._addEntity(CompositeEntity.java:2122)<br /> [null] at ptolemy.kernel.ComponentEntity.setContainer(ComponentEntity.java:518)<br /> [null] at ptolemy.kernel.CompositeEntity.setContainer(CompositeEntity.java:1857)<br /> [null] at ptolemy.actor.gui.Effigy.setContainer(Effigy.java:401)<br /> [null] at ptolemy.kernel.ComponentEntity.<init>(ComponentEntity.java:106)<br /> [null] at ptolemy.kernel.CompositeEntity.<init>(CompositeEntity.java:164)<br /> [null] at ptolemy.actor.gui.Effigy.<init>(Effigy.java:133)<br /> [null] at ptolemy.vergil.actor.DocEffigy.<init>(DocEffigy.java:60)<br /> [null] at org.kepler.gui.ShowDocumentationAction.actionPerformed(ShowDocumentationAction.java:136)<br /> [null] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012)<br /> [null] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335)<br /> [null] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404)<br /> [null] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)<br /> [null] at javax.swing.AbstractButton.doClick(AbstractButton.java:374)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:829)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:873)<br /> [null] at java.awt.Component.processMouseEvent(Component.java:6268)<br /> [null] at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> [null] at java.awt.Component.processEvent(Component.java:6033)<br /> [null] at java.awt.Container.processEvent(Container.java:2045)<br /> [null] at java.awt.Component.dispatchEventImpl(Component.java:4629)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2103)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4455)<br /> [null] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4633)<br /> [null] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4297)<br /> [null] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4227)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2089)<br /> [null] at java.awt.Window.dispatchEventImpl(Window.java:2517)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4455)<br /> [null] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:649)<br /> [null] at java.awt.EventQueue.access$000(EventQueue.java:96)<br /> [null] at java.awt.EventQueue$1.run(EventQueue.java:608)<br /> [null] at java.awt.EventQueue$1.run(EventQueue.java:606)<br /> [null] at java.security.AccessController.doPrivileged(Native Method)<br /> [null] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)<br /> [null] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116)<br /> [null] at java.awt.EventQueue$2.run(EventQueue.java:622)<br /> [null] at java.awt.EventQueue$2.run(EventQueue.java:620)<br /> [null] at java.security.AccessController.doPrivileged(Native Method)<br /> [null] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)<br /> [null] at java.awt.EventQueue.dispatchEvent(EventQueue.java:619)<br /> [null] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)<br /> [null] at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)<br /> [null] Using default context menu stuff for class: ptolemy.kernel.ComponentEntity<br /> [null] Using default context menu stuff for class: ptolemy.kernel.ComponentEntity<br /> [null] Using default context menu stuff for class: ptolemy.kernel.ComponentEntity</p> Bug #5174 (Resolved): Reduce the number of modules in Kepler CORE.https://projects.ecoinformatics.org/ecoinfo/issues/51742010-09-08T23:26:38ZDavid Welkerdavid.v.welker@gmail.com
<p>The number of modules in Kepler is a little bit overwhelming. If the user was required to specify modules.txt manually (as they would in some rarer use cases) it would be tedious at best. Given that our current module set was not developed according to completely consistent guidelines, we should develop such a set of guidelines with an eye to reducing the number of modules to make manual specification of modules more manageable.</p> Bug #4372 (Resolved): demos in doc-index.htm don't exist (Hello World, Simple Addition etc.)https://projects.ecoinformatics.org/ecoinfo/issues/43722009-09-09T17:21:11ZChristopher Brookscxh@eecs.berkeley.edu
<p>I have some visitors today and would like to show off the<br />devel version of Kepler.</p>
<p>When I start kepler, the page that comes up (configs/kepler/doc-index.htm)<br />has links for the Hello World and R demos. However, these links do not work?</p>
<p>For example:</p>
<p>java.io.FileNotFoundException: /Users/cxh/src/kepler/common/demos/getting-started/04-HelloWorld.xml (No such file or directory)<br /> at java.io.FileInputStream.open(Native Method)</p>
<p>The common/demos directory is empty?</p> Bug #4061 (Resolved): Documentation links are not activehttps://projects.ecoinformatics.org/ecoinfo/issues/40612009-05-13T01:51:56ZChristopher Brookscxh@eecs.berkeley.edu
<p>In the splash screen, none of the documentation links are active.<br /> Help -> About -> Documentation<br /> Brings up doc-index.htm<br /> That file has "Kepler Getting Started Guide" etc. None of the links are active.<br /> If we are not shipping docs, then how about a placeholder?</p>
<p>Otherwise the user does not know that we are intentionally not shipping docs.</p>
<p>This was replicated with the Installer under Mac OS X and in the SVN tree.</p> Bug #4029 (Resolved): missing dependency for tools.jar in windowshttps://projects.ecoinformatics.org/ecoinfo/issues/40292009-04-27T19:29:32ZChris Weedchrisweed@gmail.com
<p>The documentation fails to mention the need for a dependency on tools.jar in setting up building Kepler with Eclipse in Windows.</p>
<p>Since tools.jar is not by default a dependency in the JRE path, the build will give errors about a missing dependency on com.sun.javadoc in KarDoclet.java.</p>
<p>The steps to fix this in eclipse are:<br />1. Windows -> Preferences -> Java -> Installed JREs<br />2. Select the default JRE -> Edit -> Add External Jars -> [Path to JDK]/lib/tools.jar</p> Bug #3449 (Resolved): Parsing exception with escaped characters in MoML,https://projects.ecoinformatics.org/ecoinfo/issues/34492008-07-12T00:03:28Zjianwu jianwujianwu@sdsc.edu
<p>If customize an actor document with "<anystring>"? It will throw exception when you save and reopen it. If you customize actor document with "<anystring>", it can not be saved.</p>
<p>The bug originated from one of our new kepler actor which has document with "<>" string. We have transform them to <> character when it is added. It works when it is saved for the first time. But throws exception when we reopen and save as an another file. It is because the file is saved as "<anystring>" for the first time but as "<anystring>" for the second time.</p> Bug #3216 (Resolved): Demo workflows do not runhttps://projects.ecoinformatics.org/ecoinfo/issues/32162008-04-09T18:32:31ZSean Riddleswriddle@gmail.com
<p>I have run into a couple of demo workflows that don't run while checking the replacement of the embedded documentation. I will append this with more if I find them.</p>
<p>demos/ENM/GARP_MultipleSpecies-*<br />Exception - "Actor is not ready to fire. in [workflowname].SDF Director and [workflowname].Get Species/Location information.Line Reader"</p> Bug #3108 (Resolved): ENM GARP Baseline 3-Actor GARP - Browser Display demo fails with NameDuplic...https://projects.ecoinformatics.org/ecoinfo/issues/31082008-01-29T06:25:39ZChristopher Brookscxh@eecs.berkeley.edu
<p>The problems below are probably common knowledge, but I've fixed up<br />the "about:" facility so that it will traverse the demos and try to open<br />them. This makes it much easier to quickly try these out.</p>
<p>The first Ecological Niche Modeling (GARP) Workflow: <br />Baseline 3-Actor GARP -Browser Display demo fails.</p>
<p>This is the first Kepler Demo. . .</p>
<p>ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "convertTo" into a container that already contains an object with that name.<br /> at ptolemy.kernel.util.NamedList.append(NamedList.java:125)<br /> at ptolemy.kernel.util.NamedObj._addAttribute(NamedObj.java:2054)<br /> at ptolemy.kernel.util.Attribute.setContainer(Attribute.java:383)<br /> at ptolemy.kernel.util.Attribute.<init>(Attribute.java:109)<br /> at ptolemy.kernel.util.Attribute.<init>(Attribute.java:86)<br /> at ptolemy.kernel.util.AbstractSettableAttribute.<init>(AbstractSettableAttribute.java:88)<br /> at ptolemy.kernel.util.StringAttribute.<init>(StringAttribute.java:110)<br /> at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source)<br /> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)<br /> at java.lang.reflect.Constructor.newInstance(Constructor.java:494)<br /> at ptolemy.moml.MoMLParser._createInstance(MoMLParser.java:3985)<br /> at ptolemy.moml.MoMLParser._handlePropertyElement(MoMLParser.java:5068)<br /> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2784)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265)<br /> at ptolemy.actor.gui.PtolemyEffigy$Factory.createEffigy(PtolemyEffigy.java:412)<br /> at ptolemy.actor.gui.EffigyFactory.createEffigy(EffigyFactory.java:209)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:595)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:555)<br /> at ptolemy.actor.gui.HTMLViewer.hyperlinkUpdate(HTMLViewer.java:264)<br /> at javax.swing.JEditorPane.fireHyperlinkUpdate(JEditorPane.java:320)<br /> at javax.swing.text.html.HTMLEditorKit$LinkController.activateLink(HTMLEditorKit.java:827)<br /> at javax.swing.text.html.HTMLEditorKit$LinkController.mouseClicked(HTMLEditorKit.java:637)<br /> at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:212)<br /> at java.awt.Component.processMouseEvent(Component.java:5504)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)<br /> at java.awt.Component.processEvent(Component.java:5266)<br /> at java.awt.Container.processEvent(Container.java:1966)<br /> at java.awt.Component.dispatchEventImpl(Component.java:3968)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2024)<br /> at java.awt.Component.dispatchEvent(Component.java:3803)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3901)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2010)<br /> at java.awt.Window.dispatchEventImpl(Window.java:1778)<br /> at java.awt.Component.dispatchEvent(Component.java:3803)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<br /> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)</p>
<p>The third GARP demo, "3. GARP with Occurrence Data from Digir/Ecogrid" <br />also fails:<br />java.io.FileNotFoundException: C:\cxh\src\kepler\workflows\eco\garpModel_ImageJ_withData.xml (The system cannot find the file specified)<br /> at java.io.FileInputStream.open(Native Method)<br /> at java.io.FileInputStream.<init>(FileInputStream.java:106)<br /> at java.io.FileInputStream.<init>(FileInputStream.java:66)<br /> at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70)<br /> at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161)<br /> at java.net.URL.openStream(URL.java:1007)</p>
<p>There are plenty of other errors as well.</p>
<p>One quick way to check for missing demos is to use the "about:" feature<br />in ptolemyII.<br />To do this:<br />1. Start Kepler with ant run-dev<br />2. Help -> Documentation -> Kepler Introduction for Scientists<br /> -> Ptolemy Introduction -> Copyright<br />3. Select "copyright" in "Other copyrights about this configuration (may take a moment to run)." <br />4. Select "about" in "Other information about this configuration." <br />5. Select " Open the .htm, .html, .xml and .pdf " for the introScientist.htm<br />and introProgrammer.htm files.</p>
<p>It is also possible to check for sizes and centering from the same page.<br />The sizes are set for XGA (1024x768), which is the size laptop that I have<br />and Edward may or may not have.</p> Bug #2914 (Resolved): Broken link on a web pagehttps://projects.ecoinformatics.org/ecoinfo/issues/29142007-08-28T20:16:35ZBruce Charcharbw@drexel.edu
<p><a class="external" href="http://users.sdsc.edu/~altintas/codingStyle.pdf">http://users.sdsc.edu/~altintas/codingStyle.pdf</a> is mentioned on <a class="external" href="http://www.kepler-project.org/Wiki.jsp?page=SoftwareDevelopmentGuidelines">http://www.kepler-project.org/Wiki.jsp?page=SoftwareDevelopmentGuidelines</a> but it doesn't load.</p> Bug #2755 (Resolved): generateDocs replaces & with & erroneouslyhttps://projects.ecoinformatics.org/ecoinfo/issues/27552007-02-01T17:34:45ZChad Berkleyberkley@nceas.ucsb.edu
<p>When i have an entity reference like < in the documentation for an actor, after I run 'ant generateDoc', < is transformed to &lt; which is wrong. The doc system needs to be a bit smarter about translating ampersands.</p> Bug #2746 (Resolved): Documentation system does not work with java 1.6https://projects.ecoinformatics.org/ecoinfo/issues/27462007-01-24T20:49:18ZChad Berkleyberkley@nceas.ucsb.edu
<p>If you try to run 'ant generateDoc' using java 1.6, it will appear to work, but in reality, JavaDoc fails with the error "Error 1". You have to set failonerror="true" in the keplerJavadoc target to see the error. I'm not sure what is causing this but it will need to be fixed as java 1.6 becomes more popular.</p> Bug #2417 (Resolved): TRACKING: DOCUMENTATION - complete first draft of documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/24172006-04-13T23:26:00ZMatthew Brookebrooke@nceas.ucsb.edu
<p>complete first draft of documentation</p>
<p>Includes:<br />Actor Man Pages<br />Getting started guide (incl. tutorial chapters)<br />FAQ</p>
<p>(Use this bug to track dependent bugs)</p> Bug #2390 (Resolved): Documentation problem with derived actorshttps://projects.ecoinformatics.org/ecoinfo/issues/23902006-03-24T00:23:17ZDan Higginshiggins@nceas.ucsb.edu
<p>There is a problem that comes up when trying to document certain actors that<br />extend other actor classes like Source, Sink, or Transform. These examples<br />define ports called "input", "output", or both. It is useful to build new actors<br />by extending these base actor, but when one does so, the inherited ports do not<br />appear in the new class source files. Since they do not appear, a more<br />specialized use cannot be documented in JavaDoc comments in the new actor<br />extending these more basic actors.</p>
<p>One can, of course, get around this by extending TypedAtomicActor and defining<br />all ports of interest.</p> Bug #1898 (Closed): Redesign the web service harvester and create design documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/18982005-01-20T19:56:04ZIlkay Altintasaltintas@sdsc.edu
<p>A document on how to do the harvesting to fit inn with the new dynamic actor<br />loading, annotation, etc. The harvested services should not be kept in the<br />repository, and they should be updated everytime the Kepler client is loaded. We<br />probably need to have a metarepository in the end to keep track of the<br />repositories and keywords that were searched and also collect some information<br />on the user's interest.</p>