Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-02-05T21:46:20ZEcoinformatics Redmine
Redmine Bug #3132 (Resolved): Once an EML dataset gets an error in downloading, cache interface will keep...https://projects.ecoinformatics.org/ecoinfo/issues/31322008-02-05T21:46:20ZJing Taotao@nceas.ucsb.edu
<p>Somehow if an EML dataset can't get data from ecogrid server (e.g. a network glitch), kepler system will keep getting error for ever since cache system captured this error (even after restart kepler). In order to get rid of this error, we need removing cache file. This is not convenient.</p>
<p>So we need cache system not capture the error if an error happens.</p> Bug #3125 (Resolved): Preview actor issues with EMLDatasourcehttps://projects.ecoinformatics.org/ecoinfo/issues/31252008-02-02T02:13:31Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Behavior for this action is inconsistent.<br />1. Previewing when the output format is set to "As Column Vector" shows no data (blank table)<br />2. Sometimes data will be shown as just text (not in table)<br />3. Sometimes going back to a selected entity will show "Preview not available" message, when other times the preview is successful (but as plain text).<br />4. When resizing the window the table does not expand with the window.</p> Bug #3119 (Resolved): Need Installer shortcuts for Windowshttps://projects.ecoinformatics.org/ecoinfo/issues/31192008-02-01T18:58:42ZDan Higginshiggins@nceas.ucsb.edu
<p>Shortcuts for the IzPack installer system have not yet been implemented, although it is possible to create such shortcuts for Windows (and Linux).</p>
<p>Such shortcuts need to be implemented.</p> Bug #3118 (Resolved): remove "Add" button from data Sources dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/31182008-02-01T10:20:37ZMatt Jonesjones@nceas.ucsb.edu
<p>The data Sources dialog (accessible from the Search pane) has been updated to include a 'Refresh' function that obsoletes the need for the previous 'Add' function. The corresponding 'Add' button should be removed from the dialog box, and the search dialog that is brought up when clicking the Add button should be removed from the source tree as it is nw obsolete.</p> Bug #3117 (Resolved): The refresh button function in source window was messed up by a KeplerSlave...https://projects.ecoinformatics.org/ecoinfo/issues/31172008-02-01T01:28:07ZJing Taotao@nceas.ucsb.edu
<p>By accident, I left a KeplerSlaveNode entry in the ecogrid registry. However when click refresh button in source window (you can click source button on data search panel to get), nothing will show up and here is the error:<br />ERROR (org.ecoinformatics.seek.ecogrid.SearchRegistryAction:queryRegistryRewriteConfig:227) problem merging new services with existing services<br /> [java] org.ecoinformatics.seek.ecogrid.exception.InvalidEcoGridServiceException: The service type is invalid or null: KeplerSlaveNode. Couldn't be added to list<br /> [java] at org.ecoinformatics.seek.ecogrid.EcoGridServicesController.addService(EcoGridServicesController.java:187)<br /> [java] at org.ecoinformatics.seek.ecogrid.EcoGridServicesController.mergeServicesList(EcoGridServicesController.java:377)<br /> [java] at org.ecoinformatics.seek.ecogrid.SearchRegistryAction.queryRegistryRewriteConfig(SearchRegistryAction.java:224)<br /> [java] at org.ecoinformatics.seek.ecogrid.ServicesRefreshAction.actionPerformed(ServicesRefreshAction.java:39)<br /> [java] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)<br /> [java] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)<br /> [java] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)<br /> [java] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)<br /> [java] at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)<br /> [java] at java.awt.Component.processMouseEvent(Component.java:5501)<br /> [java] at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)<br /> [java] at java.awt.Component.processEvent(Component.java:5266)<br /> [java] at java.awt.Container.processEvent(Container.java:1966)<br /> [java] at java.awt.Component.dispatchEventImpl(Component.java:3968)<br /> [java] at java.awt.Container.dispatchEventImpl(Container.java:2024)<br /> [java] at java.awt.Component.dispatchEvent(Component.java:3803)<br /> [java] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)<br /> [java] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)<br /> [java] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)<br /> [java] at java.awt.Container.dispatchEventImpl(Container.java:2010)<br /> [java] at java.awt.Window.dispatchEventImpl(Window.java:1778)<br /> [java] at java.awt.Component.dispatchEvent(Component.java:3803)<br /> [java] at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<br /> [java] at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)<br /> [java] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)<br /> [java] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)<br /> [java] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)<br /> [java] at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)</p>
<p>After I deleting this entry, the everything works fine.</p> Bug #3109 (Resolved): Many demos linked to getting started don't workhttps://projects.ecoinformatics.org/ecoinfo/issues/31092008-01-29T18:56:03ZChad Berkleyberkley@nceas.ucsb.edu
<p>We need to either fix or remove the links from introScientist.htm that won't load. many are the web service ones that no longer work.</p> Bug #3102 (Resolved): Inclusion of R executable for Mac and Linux ?https://projects.ecoinformatics.org/ecoinfo/issues/31022008-01-24T23:38:15ZDan Higginshiggins@nceas.ucsb.edu
<p>We included a set of R executables for Windows as of beta3 and plan on doing so also for RC1. However, we do not include R for the Mac or Linux.</p>
<p>We need to consider whether we want to include the binaries as part of the installer. Mac installer is about 58 MB so there is a size issue. (Also do we want to include even the Windows version in CVS for nightly build?)</p>
<p>Dan Higgins - Jan 2008</p> Bug #3075 (Resolved): Fold Top,java file in $KEPLER/src/exp/ dir into Ptolemy srchttps://projects.ecoinformatics.org/ecoinfo/issues/30752008-01-16T23:59:41ZDan Higginshiggins@nceas.ucsb.edu
<p>Getting the FILE|Open menu to initially point to the $KEPLER/demos directory required a change to the PTII ptolemy/gui/Top.java file. This was done by placing a slightly modified version in the Kepler exp directory to override the Ptolemy version.</p>
<p>This version of the file should be reworked with a parameter to set the intial directory in Kepler but use the Ptolemy settings in PTII; and the resulting file folded into the Ptolemy source tree.</p> Bug #3063 (Resolved): CommandLineExec actor does not generate Exit codehttps://projects.ecoinformatics.org/ecoinfo/issues/30632008-01-11T21:41:46ZDan Higginshiggins@nceas.ucsb.edu
<p>Supposedly, the CommandLineExec actor will generate a '1' on the exitCode output when the execution of the command line is successful. Apparently this does NOT happen under Windows; nothing appears on the output if the command does not send anything to SysOut. This makes it impossible to run a command line operation in the middle of workflow and use it to trigger further actors.</p>
<p>See the example $KEPLER/workflows/eco/maxent.xml</p>
<p>Dan Higgins - Jan 2008</p> Bug #3052 (Resolved): Installer crashes with EXC_BAD_ACCESShttps://projects.ecoinformatics.org/ecoinfo/issues/30522008-01-04T00:58:38ZDavid Brooksdave@bcs.co.nz
<p>Here's the start of the crash log:</p>
<p>Host Name: djbmac<br />Date/Time: 2008-01-04 13:20:10.617 +1300<br />OS Version: 10.4.11 (Build 8S2167)<br />Report Version: 4</p>
<p>Command: Kepler_beta3_install<br />Path: /Users/dave/Desktop/Kepler_beta3_install.app/Contents/MacOS/Kepler_beta3_install<br />Parent: WindowServer [57]<br />Rosetta: Yes</p>
<p>Version: ??? (5.0)</p>
<p>PID: 9484<br />Thread: Unknown</p>
<p>Exception: EXC_BAD_ACCESS (0x0001)<br />Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x00000000</p>
<p>Thread 0:<br />0 Kepler_beta3_install 0xb80a564f 0xb8000000 + 677455<br />1 Kepler_beta3_install 0xb809fb15 0xb8000000 + 654101<br />2 Kepler_beta3_install 0xb80bd72e 0xb8000000 + 775982<br />3 Kepler_beta3_install 0xb811e403 spin_lock_wrapper + 1985</p>
<p>Thread 1:<br />0 Kepler_beta3_install 0xb822fa6b strchr + 72<br />1 Kepler_beta3_install 0xb81cb487 pthread_cond_wait + 3114<br />2 Kepler_beta3_install 0xb816765e catch_exception_raise_state_identity + 318<br />3 Kepler_beta3_install 0xb8166b9a CallPPCFunctionAtAddressInt + 177124<br />4 Kepler_beta3_install 0xb8166a91 CallPPCFunctionAtAddressInt + 176859<br />5 Kepler_beta3_install 0xb816775c catch_exception_raise_state_identity + 572<br />6 Kepler_beta3_install 0xb8200c00 pthread_create + 1124</p>
<p>Unknown thread crashed with i386 Thread State:<br />eax: 0x00000000 ebx: 0xb80a5628 ecx:0x00000000 edx: 0x00000003<br />edi: 0x00000000 esi: 0x80d03660 ebp:0xb7fff9f8 esp: 0xb7fff9c0<br /> ss: 0x0000001f efl: 0x00010206 eip:0xb80a564f cs: 0x00000017<br /> ds: 0x0000001f es: 0x0000001f fs:0x00000000 gs: 0x00000037</p> Bug #3039 (Resolved): EML2 Datasource (from search) does not include Documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/30392007-12-20T23:29:51ZDan Higginshiggins@nceas.ucsb.edu
<p>If you search Earthgrid (e.g. for 'Datos') and drag result to work area, the Documentation context menu will not show any information.<br />If you just drag a EML2 Datasource actor to the workarea, Documentation will show up OK!</p> Bug #3029 (Resolved): NPE when trying to save semantic typehttps://projects.ecoinformatics.org/ecoinfo/issues/30292007-12-14T17:23:37ZChad Berkleyberkley@nceas.ucsb.edu
<p>When trying to save a semantic type on a composite actor, I get an NullPointerException. To reproduce this bug do the following:</p>
<p>1) drag a composite to the canvas<br />2) rt. click and choose 'Semantic Type Annotation'<br />3) choose a type to add and click the >> button to add it<br />4) click "ok"</p>
<p>The ok button will pause in the depressed form then an NPE will appear on the console. The NPE looks like this:</p>
<p>[java] >>> getConceptId() = urn:lsid:localhost:onto:1:1#Actor<br /> [java] >>> getConceptId() = urn:lsid:localhost:onto:2:1#GeneralPurpose<br /> [java] >>> getConceptId() = urn:lsid:localhost:onto:2:1#Workflow<br /> [java] >>> getConceptId() = urn:lsid:localhost:onto:2:1#LocalInput<br /> [java] Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException<br /> [java] at org.kepler.sms.gui.PortSemanticTypeEditorPane.doCommit(PortSemanticTypeEditorPane.java:113)<br /> [java] at org.kepler.sms.gui.SemanticTypeEditor._doCommit(SemanticTypeEditor.java:186)<br /> [java] at org.kepler.sms.gui.SemanticTypeEditor.access$000(SemanticTypeEditor.java:53)<br /> [java] at org.kepler.sms.gui.SemanticTypeEditor$1.actionPerformed(SemanticTypeEditor.java:129)<br /> [java] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)<br /> [java] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)<br />.......</p> Bug #2959 (Resolved): Need for Multiport input for RExpression actorhttps://projects.ecoinformatics.org/ecoinfo/issues/29592007-09-10T21:32:31ZDan Higginshiggins@nceas.ucsb.edu
<p>Kevin Drury added a multiport input to an RExpression actor and noted that only the 1st channel was input. Currently, one can add a multiport input but it is not recognized as a multiport by the actor (NOTE: The Expression actor also allows one to add a multiport but does not recognize it or do anything with the multiple channels.)</p>
<p>Ideally, a multiport should probably just concatenate data from multiple attached channels.</p> Bug #2889 (Resolved): fileName in ConfigXML.java not getting sethttps://projects.ecoinformatics.org/ecoinfo/issues/28892007-07-12T00:03:22ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>ConfigXML.java has two constructors, but only one sets String fileName, the variable that points to Config.xml. This variable is used later in the SaveDOM method and must therefore be set if one wants to be able to write to the Config.xml file.</p> Bug #2712 (Resolved): Problem with EML2DataSource with extra cols in csv filehttps://projects.ecoinformatics.org/ecoinfo/issues/27122006-12-31T21:27:11ZDan Higginshiggins@nceas.ucsb.edu
<p>This problem can be seen by seaching for 'biomass'. First result is "1999 Sevilleta NPP Quadrat Sampling Data". Drag onto canvas and configure Data Output Format to return 'As Column Vector'. If you make a SDF workflow and try to display any of the columns to a Display actor the message</p>
<p>"Metadata sees data has 12columns but actually data has 13columns. Please make sure metadata is correct!"</p>
<p>Most of the rows in the table do have only 12 comma-separated columns. However, there are a few rows that have some additional comma-separated comments AFTER the 12th column value! This apparently causes a parsing failure.</p>
<p>I suggest that the parser should be modified to ignore any addition data beyond the last column. This would allow additional comments to the right of actual data columns. Note that R does this when it parses dataframes. Morpho also will display the data in this dataset without 'choking' on additional data off the right in some rows. (Dan Higgins)</p>