Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-12T18:53:40ZEcoinformatics Redmine
Redmine Kepler - Bug #4881 (New): RExpression outputs [false] for any matrix of booleanshttps://projects.ecoinformatics.org/ecoinfo/issues/48812010-03-12T18:53:40ZOliver Soongsoong@nceas.ucsb.edu
<p>In an RExpression, add an output port "out" and use this R script:</p>
<p>out <- matrix(c(TRUE, FALSE, TRUE, FALSE), 2)</p>
<p>I get [false] as the output token, which seems to be because RExpression.java on line 1108 says:</p>
<p>mt = new BooleanMatrixToken();</p>
<p>instead of:</p>
<p>mt = new BooleanMatrixToken(valS);</p>
<p>or something similar. I'm not actually sure such a constructor exists, but it seems like it should given the other constructors in the lines before.</p> Kepler - Bug #4880 (New): RExpression cannot output matrix of stringshttps://projects.ecoinformatics.org/ecoinfo/issues/48802010-03-12T18:45:03ZOliver Soongsoong@nceas.ucsb.edu
<p>Create an RExpression with the output port "out" and for the script, use:</p>
<p>out <- matrix(letters, 2)</p>
<p>Looking at the code, it seems as if a matrix of strings was never really considered. Commas in the strings would likely cause problems, and I don't actually know if there's a StringMatrixToken.</p> Kepler - Bug #4879 (New): RExpression replaces ) in string vectors with } when outputting to a porthttps://projects.ecoinformatics.org/ecoinfo/issues/48792010-03-12T18:37:49ZOliver Soongsoong@nceas.ucsb.edu
<p>In an RExpression, create the output port "out" and in the R script, use:</p>
<p>out <- c("(", ")")</p>
<p>Hooking this to a Display actor, I get {"(", "}"}. This is because RExpression.java line 1139 (I think) has:</p>
<p>temp = temp.replace(')', '}');</p>
<p>which replaces all occurrences of ), even within the string.</p> Kepler - Bug #4869 (In Progress): changes made to workflows during dialogs before committing (Edi...https://projects.ecoinformatics.org/ecoinfo/issues/48692010-03-04T19:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>When I make changes to an actor through the dialog, it seems like the changes are made to the workflow immediately, before the "Commit" button is clicked.</p>
<p>For example, create a workflow with an EML 2 Dataset actor. Make sure Kepler has not already authenticated with KNB. Now edit the EML 2 Dataset actor to reference a data package that requires authentication. The KNB login window will immediately pop up, even though no changes have been committed. Dismiss the window in some way. Now click the Help button and close the help window. The dialog will have disappeared. Open the actor dialog again, and the change will be there.</p>
<p>I should point out that the "Cancel" button does seem to work, but I suspect (based on debugging comments and comments in code) that this acts by reverting the changes already made.</p>
<p>I've seen this for sure on EML 2 Dataset and RExpression, since changes to one trigger visual feedback and I've mucked around in the code of the other. I suspect this is a general problem, though, and it may be a result of the underlying ptolemy design.</p> Kepler - Bug #4767 (Resolved): error instantiating actor with port types from KARhttps://projects.ecoinformatics.org/ecoinfo/issues/47672010-02-06T02:52:36ZOliver Soongsoong@nceas.ucsb.edu
<p>Create an Expression actor, give it an input port of type boolean, save it as a KAR into a local repository, then try and drag it onto the canvas. I get an error:</p>
<p>ptolemy.kernel.util.IllegalActionException: TypeAttribute can only be contained by instances of TypedIOPort.<br /> in .Expression.kepler:input and ._type</p> Kepler - Bug #4710 (Resolved): RExpression fails to convert arrayType(niltype)https://projects.ecoinformatics.org/ecoinfo/issues/47102010-01-29T02:09:15ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow with 2 RExpressions. The first should output c(NA, NA). The second should take the output from the first as input. Hook a Display to the output of the second to observe the error in R. Basically, a token of arrayType(niltype) is sent, but the second RExpression doesn't know how to convert this and drops the token. I think it just needs another entry of "|| (token_type_string.startsWith("arrayType(niltype"))" around line 631 of RExpression.java.</p> Kepler - Bug #4633 (Resolved): LSID conflictshttps://projects.ecoinformatics.org/ecoinfo/issues/46332009-12-15T01:04:31ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow and save a KAR (KAR1). Note the LSID. Change the workflow in some recognizable fashion and save a KAR (KAR2). The LSID bumps as expected. Close the workflow and open KAR1. Make a different change (so it's obviously not the workflow in KAR2) and save the KAR (KAR3). Notice that when the workflow reopens, it looks like KAR2 because it is KAR2 down to the MOML in KAR3.</p>
<p>I'm observing this at r22183 right now.</p> Kepler - Bug #4630 (Resolved): creating and changing relations don't trigger LSID bumphttps://projects.ecoinformatics.org/ecoinfo/issues/46302009-12-14T22:28:16ZOliver Soongsoong@nceas.ucsb.edu
<p>Make a workflow with at least 3 ports and only 2 connected. Check the LSID. Now move a relation from one port to another. The LSID is the same.</p> Kepler - Bug #4570 (Resolved): dangling file handle for KARshttps://projects.ecoinformatics.org/ecoinfo/issues/45702009-11-21T01:23:46ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not a 100% certain this is the cause, but on Windows, if I open a KAR file then close it, Kepler doesn't seem to release the file handle, which prevents me from deleting the KAR. I seem to recall having problems overwriting KAR files in the past, so this is somewhat problematic. Obviously, closing Kepler releases the file handle.</p> Kepler - Bug #4559 (Resolved): local repositories not showing up in components treehttps://projects.ecoinformatics.org/ecoinfo/issues/45592009-11-19T22:25:52ZOliver Soongsoong@nceas.ucsb.edu
<p>Summary says it all. I'm at r21772, and the default workflows repository isn't in the components tree. Adding repositories doesn't do anything. I'm not even getting prompts to sign into KNB or DEV to cache data.</p> Kepler - Bug #4529 (Resolved): NPE while saving KAR crashes Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/45292009-11-04T06:19:39ZOliver Soongsoong@nceas.ucsb.edu
<p>While exploring another bug, I encountered this NPE, and it entirely killed Kepler. This happened after saving a workflow into a local repository. I don't know specifically how to replicate it, though.</p>
<p>done writing KAR file to C:\Documents and Settings\visitor\Desktop\kepler\workflows\test1.kar<br />java.lang.NullPointerException<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:217)<br />[...]<br />ERROR (org.kepler.kar.handlers.ActorMetadataKAREntryHandler:open:235) error opening the workflow: null<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)</p> Kepler - Bug #4512 (Resolved): missing entries with multiple copies of the same KAR file in a sin...https://projects.ecoinformatics.org/ecoinfo/issues/45122009-10-28T22:43:23ZOliver Soongsoong@nceas.ucsb.edu
<p>Things don't seem to work right if I have multiple copies of the same KAR file in a single local repository. I think this is related to only one entry for an LSID being allowed in a repository.</p>
<p>If I make a file system copy of the KAR file, only one copy (the oldest?) will show up in Kepler, which could be reasonable if potentially confusing and inconvenient. I presume this is because the KAR files have identical LSIDs.</p>
<p>However, if I open the KAR in Kepler and Save Archive to create a copy, that copy will show up in Kepler, will appear to be empty (lacking XML and ROML entries), but can be opened. The original remains as before. I think this is because the KAR files have different LSIDs, but the XML and ROML files have the same.</p>
<p>Maybe this is as intended, but it's certainly confusing because the KARs look empty and the folder/KAR listing does not accurately reflect the file system structure.</p> Kepler - Bug #4510 (Resolved): can't add local repository if its name begins with the name of ano...https://projects.ecoinformatics.org/ecoinfo/issues/45102009-10-28T19:24:57ZOliver Soongsoong@nceas.ucsb.edu
<p>If I've added C:\Documents and Settings\soong\Desktop\kruger as a local repository, I can't add C:\Documents and Settings\soong\Desktop\kruger2. It complains that one is a subdirectory of the other, even though they are not.</p> Kepler - Bug #4409 (Resolved): View Documentation for an actor works oncehttps://projects.ecoinformatics.org/ecoinfo/issues/44092009-09-24T18:00:46ZOliver Soongsoong@nceas.ucsb.edu
<p>I can view the documentation for an actor in the actor library once. After that, I can no longer drag actors onto the canvas and I can no longer view any more documentation.</p>
<p>I just updated and this is observed on linux and XP.</p>
<p>Restarting Kepler seems to at least reset this.</p> Kepler - Bug #4274 (Resolved): Metacat authentication fails under trunk, not under pre-alpha branchhttps://projects.ecoinformatics.org/ecoinfo/issues/42742009-07-27T21:01:41ZOliver Soongsoong@nceas.ucsb.edu
<p>I can't search or access KNB datasets that require authentication. The console stops after: <br />ldap authenticating...<br />creating gui<br />disposing<br />Kepler then becomes unresponsive. From what I've been told, it involves problems with the LDAP, but I'm not sure it's if it's being addressed.</p>
<p>Incidentally, authentication seems to work fine in the pre-alpha branch.</p>