Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-06-25T01:12:44ZEcoinformatics Redmine
Redmine Bug #4184 (Resolved): EML 2 Dataset disregarding selectedEntity from XMLhttps://projects.ecoinformatics.org/ecoinfo/issues/41842009-06-25T01:12:44ZOliver Soongsoong@nceas.ucsb.edu
<p>1. Drag an EML 2 Dataset actor onto the canvas and change the selectedEntity field from the initial value.<br />2. Save the workflow<br />3. Close and re-open the workflow<br />4. The selectedEntity value should be the initial value again.</p> Bug #4143 (Resolved): "change failed" error while copy/paste-ing an ImageJ actorhttps://projects.ecoinformatics.org/ecoinfo/issues/41432009-06-09T23:21:26ZOliver Soongsoong@nceas.ucsb.edu
<p>This seems to affect only Windows systems and has to do with saved values in the fileOrURL parameter in the ImageJ actor. It seems to occur when the model run folder contained within the .kepler folder is deleted. To cause this to occur under Windows, create a trivial model (1 SDF, 1 RExpression, 1 ImageJ hooked to the RExpression's graphicsFileName port), run it once, then save it. Close Kepler, clean-cache, and open the model again. The actor cannot be copy/pasted.</p>
<p>The workaround is simply to delete the value in the fileOrURL parameter or find a linux/OSX system.</p> Bug #4142 (Resolved): EML 2 Dataset caches restricted datasets, allows access across sessionshttps://projects.ecoinformatics.org/ecoinfo/issues/41422009-06-09T19:05:42ZOliver Soongsoong@nceas.ucsb.edu
<p>I authenticated to search and add an EML 2 Dataset actor for a restricted data table. If I save the workflow, close Kepler, and re-open, I can run the workflow and access the data without authenticating. This seems slightly unsafe, although it may be intended.</p> Bug #4086 (Resolved): Port-Parameters half-work with composite actorshttps://projects.ecoinformatics.org/ecoinfo/issues/40862009-05-20T17:31:55ZOliver Soongsoong@nceas.ucsb.edu
<p>Under the SDF Director, I can create a Composite Actor containing a Port-Parameter and a Display actor. There are 4 cases, which will be attached:</p>
<p>1. Port-Parameter is directly linked to a Display actor. Kepler error.<br />2. Port-Parameter is directly linked to a Display actor, an Expression actor in the outer workflow is directly linked to the Port-Parameter. Works as expected.<br />3. Port-Parameter not linked to the Display actor, an Expression in the Composite Actor that repeats the Port-Parameter value is directly linked to the Display actor. No Expression actor in the outer workflow. Works as expected.<br />4. Port-Parameter not linked to the Display actor, an Expression in the Composite Actor that repeats the Port-Parameter value is directly linked to the Display actor, an Expression actor in the outer workflow is directly linked to the Port-Parameter. Kepler error.</p> Bug #4069 (Resolved): Metacat Authenticated Query fails for specific user/group/dataset combinationshttps://projects.ecoinformatics.org/ecoinfo/issues/40692009-05-15T19:02:12ZOliver Soongsoong@nceas.ucsb.edu
<p>The problem affects several datasets with similar access permissions, such as judithk.769.12.</p>
<p>These datasets are not publicly accessible, but access is granted to the kruger-tpc group: <br />[read] cn=kruger-tpc,o=NCEAS,dc=ecoinformatics,dc=org</p>
<p>My login is part of the group, and I can view the datasets through the KNB webpage and through Morpho.</p>
<p>If I enable the Metacat Authenticated Query in Kepler and provide my login credentials, I do not see the datasets. Regetz confirmed this, but he was able to search for a private dataset of his own. Derik also confirmed that he was able to access some private data. The problem occurs on OSX, linux, and Windows for both 1.x dev and 1.0.0.</p> Bug #4033 (Resolved): Can't compile, MakeKars not foundhttps://projects.ecoinformatics.org/ecoinfo/issues/40332009-04-29T02:22:21ZOliver Soongsoong@nceas.ucsb.edu
<p>I can't get the head to build, and the compiler is complaining it can't find MakeKars. Revision 17442 will compile, though. This is with XP, kepler-trunk, having just done svn update and ant update.</p>
<p>Z:\kepler\modules\loader\src\org\kepler\core\loader\Loader.java:34: package org.kepler.build does not exist<br />import org.kepler.build.MakeKars;<br /> ^</p> Bug #3988 (Resolved): Rectangle shifts position on resizehttps://projects.ecoinformatics.org/ecoinfo/issues/39882009-04-17T19:11:11ZOliver Soongsoong@nceas.ucsb.edu
<p>If I create a rectangle (components->workflow->workflow documentation) and resize it, the entire rectangle shifts slightly up and left.</p> Bug #3986 (Resolved): RExpression confounding R working directory and .kepler folderhttps://projects.ecoinformatics.org/ecoinfo/issues/39862009-04-15T01:22:29ZOliver Soongsoong@nceas.ucsb.edu
<p>If I have two RExpression actors, I might expect them to operate in different working directories, yet still be able to pass data from one to the other. This fails, as shown in the example at the URL.</p>
<p>NOTE: The example will first fail because of another bug. To see this problem, you have to first do the workaround described in the second comment of bug 3985.</p> Bug #3984 (Resolved): RequireVersion parameter cannot be deleted from a saved workflowhttps://projects.ecoinformatics.org/ecoinfo/issues/39842009-04-14T18:16:48ZOliver Soongsoong@nceas.ucsb.edu
<p>In an unsaved workflow (no associated file), RequireVersion can be added and deleted as expected. If I save an entirely empty workflow to a file, I can add RequireVersion but cannot delete it. The URL is an example workflow.</p> Bug #3912 (Resolved): RExpression actor has a single line text entry fieldhttps://projects.ecoinformatics.org/ecoinfo/issues/39122009-03-20T22:37:27ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.x dev Rev. 17126 from svn</p>
<p>The RExpression actor source entry is only a single line. It does not convert pasted newlines into in the XML.</p>
<p>Current the actor's XML has this bit:</p>
<p><property name="expression" class="ptolemy.kernel.util.StringAttribute" value="a <- c(1,2,3,5) plot(a)"><br /> <display name="R function or script"/><br /></property><br /><property name="_editorFactory" class="ptolemy.vergil.toolbox.TextEditorTableauFactory"><br /> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression"><br /> </property><br /> <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="80"><br /> </property><br /> <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="40"><br /> </property><br /></property></p>
<p>Replacing that bit of XML with the following, based on older RExpression actors, seems to work:</p>
<p><property name="expression" class="ptolemy.kernel.util.StringAttribute" value="a <- c(1,2,3,5) plot(a)"><br /> <display name="R function or script"/><br /> <property name="R Expression" class="ptolemy.actor.gui.style.TextStyle"><br /> <property name="height" class="ptolemy.data.expr.Parameter" value="20"><br /> </property><br /> <property name="width" class="ptolemy.data.expr.Parameter" value="80"><br /> </property><br /> </property><br /></property></p> Bug #3910 (Resolved): RExpression multiport input drops record columnshttps://projects.ecoinformatics.org/ecoinfo/issues/39102009-03-19T19:27:25ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org</p>
<p>Sending multiple records to the RExpression actor via a multiport input does not work as expected. With a single record, it behaves as expected. With two different records, it seems to drop the last column from each. If the two records come from the same source, the actor behaves as expected. If the two records come from different sources but contain the same data, the actor behaves as expected. With three different records, it seems to drop the first and last column. If the three records come from the same source, the actor behaves as expected. If the three records come from different sources but contain the same data, the actor behaves as expected. If only two of the three records contain unique data, then the actor drops the last column from all three.</p>
<p>The URL points to a workflow demonstrating the problem.</p> Bug #3909 (Resolved): RExpression fails with certain port nameshttps://projects.ecoinformatics.org/ecoinfo/issues/39092009-03-19T19:08:01ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org</p>
<p>Port names that are not simple R names causes the RExpression actor to fail with the error message that R cannot be found. The error message is misleading, and the variable names could still be used through the assign function. Escaping the name with backquotes will work in nearly all cases, but I think the assign function is slightly more robust.</p> 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> Bug #3892 (Resolved): EML 2 Dataset file path confusionhttps://projects.ecoinformatics.org/ecoinfo/issues/38922009-03-16T22:39:23ZOliver Soongsoong@nceas.ucsb.edu
<p>Kepler 1.0.0, Java 1.6.0_11, XP 64-bit</p>
<p>The EML 2 Dataset actor parameters EML File and Data File look for file paths. If I open a new workflow, add the EML 2 Dataset actor, and browser to two files, their full paths are recorded in the actor. I can save this workflow and open it with no problems.</p>
<p>If I place the saved workflow in the same folder as the EML and data files, open the saved workflow, edit the EML 2 Dataset actor, and browse to the same two files, then the full paths are replaced with local paths relative to the workflow's xml file (i.e., just the filename). If I save this modified workflow and try to reopen it, I get an error:</p>
<p>Data entity : Dailyrain1992.txt, failed to be downloaded and please check the data link in metadata</p>
<p>The URL is a zip of four files: <br />EML file: judithk.609.21.xml<br />Data file: judithk.657.1-Dailyrain1980.txt<br />first workflow (no error on load): full path.xml<br />second workflow (error on load): filename only.xml</p> Bug #3890 (Resolved): EML 2 Dataset has trouble with a certain data tablehttps://projects.ecoinformatics.org/ecoinfo/issues/38902009-03-16T20:49:59ZOliver Soongsoong@nceas.ucsb.edu
<p>Kepler 1.0.0, Java 1.6.0_11, XP 64-bit</p>
<p>Kepler has difficulty with table Dailyrain2004.txt from judithk.609.21 in KNB. The workflow at the URL is simply the EML 2 Dataset actor for that table and nothing else. The error message is not particularly helpful.</p>