Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-01-19T00:08:30ZEcoinformatics Redmine
Redmine Bug #3078 (Resolved): No documentation for the 'SSH to Execute' actorhttps://projects.ecoinformatics.org/ecoinfo/issues/30782008-01-19T00:08:30ZDan Higginshiggins@nceas.ucsb.edu
<p>No documentation appear for the 'SSH to Execute' actor (org.sdm.spa.Ssh2Exec)</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 #3036 (Resolved): Need to be able to delete actors from the libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/30362007-12-18T22:48:29ZDan Higginshiggins@nceas.ucsb.edu
<p>We can now add a customized or new actor to the user library, but there is no way to remove actors without deleting the entire .kepler directory (or at lease the part with actor info).</p>
<p>Need a "Delete Selected Actor" menu, perhaps as a context menu (popup) menu item?</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 #3026 (Resolved): Actor documentation does not appear in older workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/30262007-12-12T23:32:19ZDan Higginshiggins@nceas.ucsb.edu
<p>Attempting to get actor documentation does not work in several of the older workflows, especially some in the demos directory. This is apparently due the fact that documentation is now saved inside kar files. This was changed after some existing workflows were created. They need to be rebuilt so that documentation will be added to the moml file for the workflow. (The documetation does show up when a new version of the actor is dragged to the workflow.)</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 #2872 (Resolved): md5 checksumshttps://projects.ecoinformatics.org/ecoinfo/issues/28722007-06-11T23:16:45ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>We should add md5 checksums to our releases.</p> Bug #2853 (Resolved): Documentation (where to save it; customization)https://projects.ecoinformatics.org/ecoinfo/issues/28532007-05-24T20:15:20ZDan Higginshiggins@nceas.ucsb.edu
<p>Kepler actors now have documentation stored in the kar files under a 'KeplerDocumentation' parameter. However, when you right click on the background of a workflow and select "Documentation/Customize', the documentation for a workflow get stored in the workflow moml under the property "DocAttribute" rather than the 'KeplerDocumentation'. This works fine for workflows but we have documentation in two different places.</p>
<p>Also, with actor documentation stored as a 'KeplerDocumentation' parameter, customizing the documentation (with the menu 'Documentation/Customize' no longer works! This is particularly a problem with customizing RExpression actors.</p>
<p>There is also the issue of what documentation is used in the repository.</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> Bug #2531 (Resolved): The link from Kepler intro page to the Ptolemy quick links page is brokenhttps://projects.ecoinformatics.org/ecoinfo/issues/25312006-08-31T12:44:41ZIlkay Altintasaltintas@sdsc.edu
<p>The Ptolemy quick links page doesn't pop up from the Kepler intro page (Getting Started link from the start up window). I don't know who is in charge of the splash screen after Matthew and Nandita. So I assigned it to myself for now.</p> Bug #2318 (Resolved): Copyrights and licenses of subpackages need to be handledhttps://projects.ecoinformatics.org/ecoinfo/issues/23182005-12-14T02:41:42ZChristopher Brookscxh@eecs.berkeley.edu
<p>Just so we don't forget, I'm submitting the copyright issue as a bug.</p>
<p>As a proposed feature, I modified the Kepler configuration.xml and<br />added copyright.htm so that Kepler can take advantage of the Ptolemy<br />II about: facility that helps handle copyright issues.</p>
<p>The problem is that packages such as Ptolemy and Kepler include<br />copyrighted software from various sources. Each package has<br />a different copyright that usually must be displayed somewhere<br />in the release.</p>
<p>I hacked up the about:copyright facilty to help handle this. The<br />current implementation is not perfect, but it helps.</p>
<p>Here's how it works.</p>
<p>If a URL starts with "about:", then code in ptolemy.actor.gui<br />specially interprets it.</p>
<p>"about:copyright" creates a page that includes links to some base<br />copyrights, such as the Ptolemy copyright and the Aelfred copyright.<br />It also looks for particular actors and if those actors are found, it<br />includes a link to the appropriate copyright. One issue here is<br />that searching for the actors can take time, the user might notice a lag.</p>
<p>If the configuration includes a property called _applicationCopyrights<br />then that the value of that parameter is assumed to be an array of<br />records of the form
{{actor="dot.separated.actor.class.name", copyright="relative/url/to/copyright.\<br />htm"}...}</p>
<p>So, if the util.ImageJActor actor is present, then going to about:copyright<br />will include a link to the javadoc and also to imagej-copyright.htm<br />imagej-copyright.htm does not currently exist, but usually this file<br />would include the ImageJ jar file copyright.</p>
<p>One issue as that the link to the javadoc defaults to pointing to the<br />Ptolemy website if the documentation cannot be found. We could add<br />yet another parameter that would send this traffic to the Kepler website.<br />I'll do this later.</p>
<p>So, to try this out, update your Kepler tree, run "ant run-dev" <br />and then at the bottom of the intro.htm, follow the<br />"This software is protected by this license." link.</p>
<p>On the Kepler copyright page, follow the link at the bottom:<br />"Kepler is based on Ptolemy II" <br />This will bring you to the about:copyright page.</p>
<p>On other cool feature is at the bottom of the Kepler copyright page<br />is "Other information about this configuration"</p>
<p>This brings up a page that includes a link (about:configuration) to<br />expand the configuration, which is a good way to quickly test for<br />missing classes. For Kepler, this will not expand to include all the<br />actors the way it does under Ptolemy, but it still has value.</p>
<p>There are also links to expand all the .xml files listed in a file.<br />For example, "about:demos#ptolemy/configs/kepler/intro.htm" <br />will expand all the workflows listed on the Kepler splash page.<br />One can then run all the demos.</p>
<p>Also, "about:links#ptolemy/configs/kepler/intro.htm" will open<br />up all the .htm, .pdf and .xml links on the splash page, which<br />is a good way to check documentation.</p>
<p>In both cases, the expansion is only one level deep, but I use it<br />all the time to check releases.</p>
<p>I don't think this is a perfect solution but it can be used to<br />help address the copyright problem. Further refinement would help.<br />What would need to be done is that for each actor that uses a third<br />party jar file we would need to create a web page that includes<br />the copyright. This takes quite a bit of work, but helps ensure<br />that the copyright is actually shipped with the release.</p>
<p>If this utility is not of interest, then feel free to remove<br />the link at the bottom of copyright.htm.</p>