Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-07-23T16:03:06ZEcoinformatics Redmine
Redmine Kepler - Bug #4261 (Resolved): Long file name on windowshttps://projects.ecoinformatics.org/ecoinfo/issues/42612009-07-23T16:03:06ZChris Weedchrisweed@gmail.com
<p>When I tried to copy my directory of the kepler source files to a windows box, I got an error about a long filename and the copy quit. The file is:<br />ConstraintCheck_FSM_MultiplePorts_MultipleStates_Transitions_NoActions.xml</p> Kepler - Bug #4215 (Resolved): Error when check out provenance with change-tohttps://projects.ecoinformatics.org/ecoinfo/issues/42152009-07-01T14:54:09ZChris Weedchrisweed@gmail.com
<p>When I tried to check out the provenance suite this week I got the error:<br />[change-to] Error: The name you specified is not a suite.</p>
<p>I ran "ant change-to -Dsuite=provenance",</p>
<p>Here is the total output:</p>
<p>C:\kepler-build\build-area>"%ANT_HOME%/bin/ant" change-to -Dsuite=provenance<br />Buildfile: build.xml</p>
<p>change-to:<br />[change-to] Retrieving modules....<br />[change-to]<br />[change-to] provenance:<br />[change-to] Downloading provenance...<br />[change-to] svn co <a class="external" href="https://code.kepler-project.org/code/kepler/trunk/modules/pro">https://code.kepler-project.org/code/kepler/trunk/modules/pro</a><br />venance C:\kepler-build\provenance<br />[change-to] A C:\kepler-build\provenance\modules-info<br />[change-to] A C:\kepler-build\provenance\modules-info\modules.txt<br />[change-to] A C:\kepler-build\provenance\lib<br />[change-to] A C:\kepler-build\provenance\lib\exe<br />[change-to] A C:\kepler-build\provenance\src<br />[change-to] A C:\kepler-build\provenance\src\org<br />[change-to] A C:\kepler-build\provenance\src\org\kepler<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\PortConnec<br />tor.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\RecordingP<br />arameters.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\Provenance<br />Event.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\Execution.<br />java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui\Proven<br />anceConfigureAction.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui\Proven<br />anceConfigurer.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui\Proven<br />anceConfigurerDialog.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui\img<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui\img\pr<br />ov_off.gif<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui\img\pr<br />ov_on.gif<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\gui\img\pr<br />ov_ov.gif<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\Recording.<br />java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\SQLRec<br />ordingParameters.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\SQLQue<br />ryV8.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\Schema<br />s.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\SQLRec<br />ordingV7.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\RegEnt<br />ity.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\SQLRec<br />ordingV8.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\SQLRec<br />ording.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\Link.j<br />ava<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\S<br />chema.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\M<br />ySQL.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\O<br />racle.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\D<br />atabaseType.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\H<br />SQL.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\T<br />able.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\D<br />atabaseFactory.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\sql\util\C<br />olumn.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\Specificat<br />ion.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\TextFileRe<br />cording.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\QueryExcep<br />tion.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\Evolution.<br />java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\Provenance<br />Recorder.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\FireState.<br />java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\Queryable.<br />java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\RecordingE<br />xception.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\kar<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\kar\Upload<br />KarToRepositoryNoGUI.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\kar\Export<br />RunsToKAR.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\provenance\XMLRecordi<br />ng.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\objectmanager<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\objectmanager\cache<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\objectmanager\cache\W<br />orkflowRunCacheObject.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\module<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\module\provenance<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\module\provenance\Ini<br />tialize.java<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\util<br />[change-to] A C:\kepler-build\provenance\src\org\kepler\util\WorkflowRun.java</p>
<p>[change-to] A C:\kepler-build\provenance\configs<br />[change-to] A C:\kepler-build\provenance\configs\ptolemy<br />[change-to] A C:\kepler-build\provenance\configs\ptolemy\configs<br />[change-to] A C:\kepler-build\provenance\configs\ptolemy\configs\kepler<br />[change-to] A C:\kepler-build\provenance\configs\ptolemy\configs\kepler\prove<br />nance<br />[change-to] A C:\kepler-build\provenance\configs\ptolemy\configs\kepler\prove<br />nance\sql.properties<br />[change-to] A C:\kepler-build\provenance\configs\ptolemy\configs\kepler\prove<br />nance\recordingTypes.properties<br />[change-to] A C:\kepler-build\provenance\resources<br />[change-to] A C:\kepler-build\provenance\resources\system.properties<br />[change-to] A C:\kepler-build\provenance\resources\kar<br />[change-to] A C:\kepler-build\provenance\resources\kar\ProvenanceRecorder<br />[change-to] A C:\kepler-build\provenance\resources\kar\ProvenanceRecorder\Pro<br />venanceRecorder.xml<br />[change-to] A C:\kepler-build\provenance\resources\kar\ProvenanceRecorder\MAN<br />IFEST.MF<br />[change-to] U C:\kepler-build\provenance<br />[change-to] Checked out revision 19601.<br />[change-to]<br />[change-to] Error: The name you specified is not a suite.</p>
<p>BUILD FAILED<br />Warning: Could not find file C:\kepler-build\provenance\module-info\modules.txt<br />to copy.</p>
<p>Total time: 33 seconds</p> Kepler - Bug #4147 (Resolved): Error message with selectable texthttps://projects.ecoinformatics.org/ecoinfo/issues/41472009-06-11T18:38:48ZChris Weedchrisweed@gmail.com
<p>When Kepler displays an error message in the pop-up dialog, the text is not selectable so I can copy-paste it into an email. This makes it tedious to report errors or problems, because I have to retype the whole message.</p> Kepler - Bug #4123 (Resolved): Image reader can't read URLhttps://projects.ecoinformatics.org/ecoinfo/issues/41232009-06-02T17:01:10ZChris Weedchrisweed@gmail.com
<p>In ptolemy.actor.lib.image.ImageReader<br />replace<br />_image = new ImageIcon(_fileRoot).getImage();</p>
<p>with:<br />try {<br /> _image = ImageIO.read(_url);<br />} catch (IOException e) {<br /> throw new IllegalActionException(this,e.toString());<br />}<br />if(!_image)
{<br /> throw new IllegalActionException(this,"Could not read file or URL: "+_url.toString());<br />}</p> Kepler - Bug #4118 (Resolved): Web Service Actor stored in Libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/41182009-05-29T16:26:25ZChris Weedchrisweed@gmail.com
<p>After setting the wsdl and service name in org.sdm.spa.WebService and org.sdm.spa.WSWithComplexTypes, I store them back in the library.<br />I then drag these new actors into the workflow desktop.<br />For WebService I get the error:<br />Change Failed<br />String index out of range: -5</p>
<p>For WSWithComplexTypes I get the error:<br />Error encountered in:<br /><property name="_type" class="ptolemy.actor.TypeAttribute" value="string"><br />TypeAttribute can only be contained by instances of TypedIOPort.<br />in .My WSWithComplexTypes.kepler:query and ._type</p>
<p>For WebService this seems to be a problem with setting the methodName parameter before setting the url parameter.<br />I was able to add a check on _urlStr to avoid this:</p>
<p>Line 410:<br />// System.out.println("Method name before get expression: " +<br />// _methodNameStr);<br />_methodNameStr = methodName.getExpression();<br />_debug("<METHOD_NAME>" + _methodNameStr + "</METHOD_NAME>");<br />// System.out.println("Method name after get expression: " +<br />// _methodNameStr);<br />int slashIndex = _urlStr.lastIndexOf('/');<br />//if(_urlStr.length()>0)
{<br />_wsName = _urlStr.substring(slashIndex + 1,<br /> _urlStr.length() - 5);<br />}</p>
<p>For WSWithComplexType I don't know the problem.<br />Chris</p> Kepler - Bug #4109 (Resolved): File Reader error message incorrecthttps://projects.ecoinformatics.org/ecoinfo/issues/41092009-05-26T21:51:12ZChris Weedchrisweed@gmail.com
<p>The "File Reader" actor (ptolemy.actor.lib.io.FileReader) prints a message<br />"Failed to write '" + fileOrURL + "'"</p>
<p>when it should be "Failed to read '" + fileOrURL + "'"</p>
<p>This is very confusing.</p> Kepler - Bug #4057 (New): UserInteractiveShell messagehttps://projects.ecoinformatics.org/ecoinfo/issues/40572009-05-08T14:46:03ZChris Weedchrisweed@gmail.com
<p>The message in the UserInteractiveShell doesn't make sense, and gives a "null" at the beginning.</p>
<p>Here is the current message:<br />The outputs of the previous step.<br />Please double click on your selections to be sent to the next step</p>
<p>This seems to come from DoubleShellTextAreaPanel.</p>
<p>I would expect it just to print my input message.</p> Kepler - Bug #4029 (Resolved): missing dependency for tools.jar in windowshttps://projects.ecoinformatics.org/ecoinfo/issues/40292009-04-27T19:29:32ZChris Weedchrisweed@gmail.com
<p>The documentation fails to mention the need for a dependency on tools.jar in setting up building Kepler with Eclipse in Windows.</p>
<p>Since tools.jar is not by default a dependency in the JRE path, the build will give errors about a missing dependency on com.sun.javadoc in KarDoclet.java.</p>
<p>The steps to fix this in eclipse are:<br />1. Windows -> Preferences -> Java -> Installed JREs<br />2. Select the default JRE -> Edit -> Add External Jars -> [Path to JDK]/lib/tools.jar</p> Kepler - Bug #4025 (Resolved): XSLTActor accepts StringToken as inputhttps://projects.ecoinformatics.org/ecoinfo/issues/40252009-04-24T13:45:47ZChris Weedchrisweed@gmail.com
<p>The input to the XSLTActor (org.sdm.spa.XSLTActor) is XML, which should be passed in as an XMLToken. However, the XSLTActor currently only accepts StringToken on it's input.</p> Kepler - Bug #3970 (Resolved): XSLT unnecessarily writes to a filehttps://projects.ecoinformatics.org/ecoinfo/issues/39702009-04-10T15:31:14ZChris Weedchrisweed@gmail.com
<p>Instead of creating a temporary file that may fail, write the XSLT output to a string buffer.<br />//XSLT.java</p>
<p>StringWriter sw = new StringWriter();</p>
<p>// Executes the Transformer<br />try {<br /> transformer.transform(xml, new StreamResult(sw));<br /> htmlStr = sw.toString();<br />} catch (Exception e) {<br /> MessageHandler.error("Transform error", e);<br />}</p> Kepler - Bug #3968 (Resolved): XSLTActor temporary file bughttps://projects.ecoinformatics.org/ecoinfo/issues/39682009-04-09T20:41:52ZChris Weedchrisweed@gmail.com
<p>The XSLTActor creates a temporary file in the current directory for storing the input XML file to be processed. This files should be created in the system temporary file directory using the method "createTempFile" in Java.io.File.</p> Kepler - Bug #3899 (New): web service actor does not work through proxyhttps://projects.ecoinformatics.org/ecoinfo/issues/38992009-03-17T19:19:25ZChris Weedchrisweed@gmail.com
<p>The run script does not set up the java proxy settings, so anything that needs to connect to the internet through http fails.</p>
<p>I had to edit kepler.sh to be the following:<br />java -Xmx512m -Xss5m -Dhttp.proxyHost=proxy -Dhttp.proxyPort=8080 -DKEPLER="$KEP" -DKEPLER_DOCS="$KEP" -Djava.endorsed.dirs=./lib/jar/base-jars/apache -Djava.library.path=./lib org.kepler.loader.Kepler $*</p>
<p>However, this needs a more elegant solution, such as an environment variable, to allow the user to set this.</p>