Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-12-09T00:28:09ZEcoinformatics Redmine
Redmine Metacat - Bug #4610 (New): trying to register a dataset when logged in asks for another authentic...https://projects.ecoinformatics.org/ecoinfo/issues/46102009-12-09T00:28:09ZOliver Soongsoong@nceas.ucsb.edu
<p>I log into KNB, then go to Register your dataset online, and it says I must register. The register dataset page seems to be ignoring the existing credentials.</p> Metacat - Bug #4609 (New): when viewed with saved credentials, KNB homepage shows blank entrieshttps://projects.ecoinformatics.org/ecoinfo/issues/46092009-12-09T00:23:12ZOliver Soongsoong@nceas.ucsb.edu
<p>I sign into the KNB, then close the window (but not the browser). The cookie persists, so when I go back to the KNB home page, it picks up the saved credentials from earlier. However, the login space shows no entries (blank username and password, -- choose one -- for the organization), so I can't be sure who I'm logged in as.</p>
<p>This also happens with dev.nceas.ucsb.edu.</p> Kepler - Bug #4569 (Resolved): viewing report before executing sometimes generates persistent bla...https://projects.ecoinformatics.org/ecoinfo/issues/45692009-11-21T01:14:11ZOliver Soongsoong@nceas.ucsb.edu
<p>I unfortunately can't figure out how to replicate this yet. It occurred with the latest tpc01 report archive, although I'm not certain it's truly specific to this KAR. After debugging the workflow and building the report, I found that opening the archive and viewing the report would not trigger a message saying the workflow needed to be run first. Executing the workflow would then generate a single blank page with no title or any content, but with a time and date stamp at the bottom. I have attached the run archive with that output in it.</p>
<p>A clean-cache made the problem go away, but I can't replicate it, so I can't be sure what went wrong or that it won't happen again.</p> Kepler - Bug #4549 (In Progress): String Replace actor "remembers" previous execution valueshttps://projects.ecoinformatics.org/ecoinfo/issues/45492009-11-14T00:56:45ZOliver Soongsoong@nceas.ucsb.edu
<p>1. Build a workflow with an SDF director (set iterations to 1), an RExpression (turn off graphics output), and a Display actor. Hook the RExpression graphicsFileName port to the Display input port.<br />2. Run this workflow. There should be no noticeable output, as no token was passed to the Display actor. An Rplots.pdf file should have been generated in the appropriate subfolder of .kepler.<br />3. Add a String Replace actor. Hook the RExpression graphicsFileName port to the String Replace stringToEdit port, and hook the String Replace output port to the Display input port.<br />4. Run this workflow. Notice now that a Display actor window opens. A blank token of some sort was passed to the Display actor (I it's a "" string token). Again, another Rplots.pdf file should have been generated.<br />5. Turn on graphics output in the RExpression and run the workflow. The expected RExpression-1.png file should have been generated, and the Display actor should open and display the filename. Pay attention to the timestamp on the folder.<br />6. Turn off graphics output in the RExpression and run the workflow. The Display actor should open again and display the png filename from the previous execution. If you browse the .kepler, you should see the correct folder with the expected Rplots.pdf file.</p> Kepler - Bug #4548 (Resolved): string tokens with newlines print the escape sequenceshttps://projects.ecoinformatics.org/ecoinfo/issues/45482009-11-13T23:11:17ZOliver Soongsoong@nceas.ucsb.edu
<p>This was first noticed when viewing an RExpression's "output" port. The output port emits a string token containing a section of the RExpression's stdout stream, with newlines encoded in the relevant OS's format. The report will then display literal "\n" or "\r\n" in the report, rather than the appropriate newlines.</p>
<p>While much of reporting ignores newlines (text boxes, for example), it might be useful to respect them here, since the RExpression output is less useful without them.</p> Kepler - Bug #4545 (Resolved): String To Image Converter seems brokenhttps://projects.ecoinformatics.org/ecoinfo/issues/45452009-11-13T22:44:42ZOliver Soongsoong@nceas.ucsb.edu
<p>If I pass the an image file as a string ("C:/tmp/image.png") to the String To Image Converter actor, it seems not to work. The output to a Display actor is:</p>
<p>{type="class ptolemy.data.AWTImageToken" width="-1" height="-1"}</p>
<p>This occurs on all OSes.</p> Kepler - Bug #4511 (Resolved): There are 2 toolbars in the Kepler main windowhttps://projects.ecoinformatics.org/ecoinfo/issues/45112009-10-28T20:46:23ZOliver Soongsoong@nceas.ucsb.edu
<p>There are 2 toolbars in the Kepler main window, one of which is empty. I've seen this using wrp on Windows and linux. If you drag the main toolbar from its docked location, it is possible to drag a second empty toolbar from the docked area by clicking in just the right place between the menu bar and the tab bars.</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 #4361 (New): Workflow Run Manager column "Workflow Name" can be confusinghttps://projects.ecoinformatics.org/ecoinfo/issues/43612009-08-31T23:41:54ZOliver Soongsoong@nceas.ucsb.edu
<p>This is a general problem with workflow naming that seems to come up here. Consider two of the attachments to <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4359">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4359</a>, CalledModel.xml and CalledModelCopy.xml. The files are identical, and differ only in filename. If I open both, Kepler will display the different filenames in the window title. If I run both, though, they show up in the Workflow Run Manager with the same name.</p>
<p>The problem is that there is the filename and there is the workflow name saved in the XML. I'm not sure how significant a problem this might be in practice, but I know I tend to rename files on my computer a lot.</p> Kepler - Bug #4358 (New): variable setter seems to lock Kepler in the wrapping up stage of a work...https://projects.ecoinformatics.org/ecoinfo/issues/43582009-08-31T22:15:15ZOliver Soongsoong@nceas.ucsb.edu
<p>Running the attached workflow seems to cause Kepler to freeze at Wrapping Up. I'm not sure if I just need to wait (for a really long time) or whether there's some other issue.</p> Kepler - Bug #4357 (Resolved): Workflow Run Manager does not mark last failed execution redhttps://projects.ecoinformatics.org/ecoinfo/issues/43572009-08-31T21:41:30ZOliver Soongsoong@nceas.ucsb.edu
<p>The workflow run manager is supposed to highlight failed executions in red. If I run a workflow and it fails, though, it is not highlighted. If I run it again, then the first failure is highlighted but not the second. If I run it again, then the first two are highlighted, but not the third. If I close and re-open Kepler, all failures are highlighted. It seems that highlighting is not updated after an execution.</p> Metacat - Bug #4301 (New): sessionid in the URL creates end-user difficultyhttps://projects.ecoinformatics.org/ecoinfo/issues/43012009-08-10T22:34:04ZOliver Soongsoong@nceas.ucsb.edu
<p>Using a plain URL, one cannot access datasets that require authentication. Alternatively, a link of the form <a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&docid=judithk.594">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&docid=judithk.594</a> will function properly when authenticated, although this form is not actually presented in metacat. However, attempting to view the metadata for any of the included data tables will insert a &sessionid= with no value, which causes an error as I think this overrides the (correctly authenticated) value that would otherwise have been passed.</p>
<p>Perversely enough, at the top of any data package is a printed URL of the form <a class="external" href="http://knb.ecoinformatics.org/knb/metacat/judithk.594.26/knb">http://knb.ecoinformatics.org/knb/metacat/judithk.594.26/knb</a>, even though the actual link is <a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&sessionid=________________________________&docid=judithk.594.26">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&sessionid=________________________________&docid=judithk.594.26</a> with the actual sessionid embedded in the URL. I think it would be safer and more robust if that sessionid were not explicitly inserted anywhere. From what I recall and have been told, everything should function as intended by simply removing the sessionid from the various URLs.</p> Kepler - Bug #4129 (Resolved): "unable to parse the metadata: null" with dataset judithk.306.21https://projects.ecoinformatics.org/ecoinfo/issues/41292009-06-05T23:59:02ZOliver Soongsoong@nceas.ucsb.edu
<p>This error occurs on XP but does not occur on linux. It only occurs if the dataset has not been previously cached. It also only seems to occur with a specific workflow, which will be attached.</p>
<p>I'm not entirely sure, but this problem can sometimes occur along with "selected Entity in momol cound't be found" errors.</p> Kepler - Bug #3985 (Resolved): Types resolved to unacceptable typeshttps://projects.ecoinformatics.org/ecoinfo/issues/39852009-04-15T00:46:31ZOliver Soongsoong@nceas.ucsb.edu
<p>URL provides a sample workflow that has been demonstrating the error on my system. Because this problem has been confusingly inconsistent in the past, I'm not 100% convinced it will produce an error for others, but it seems to be causing problems on three builds on my system, two builds in a VM, and two systems in the vislab here, so hopefully I won't be alone this time. It's affecting both 1.0.0 and 1.x dev.</p> Kepler - Bug #3901 (Resolved): unescaped & in <entity name="a & b"> on line 4https://projects.ecoinformatics.org/ecoinfo/issues/39012009-03-18T02:08:48ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org</p>
<p>If a workflow is saved with an & in the file name, even though the file name is valid in the file system, Kepler throws an exception because the name attribute is unescaped in the outermost TypedCompositeActor entity. If Kepler is trying to re-open the workflow similar to how a save as is handled, then it's choking while attempting to parse the file. The & should be escaped as & in the name attribute, I think.</p>