Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-28T00:15:15ZEcoinformatics Redmine
Redmine Bug #5699 (New): Change the workflow scheduler server documentation link in the workflow-schedule...https://projects.ecoinformatics.org/ecoinfo/issues/56992012-08-28T00:15:15ZJing Taotao@nceas.ucsb.edu
<p>Currently the the workflow scheduler server documentation points to the svm trunk version. In the next workflow-scheduler-gui release, the documenation should be a branch or tag version.</p> Bug #5586 (New): Get newest version of local files in EML actorhttps://projects.ecoinformatics.org/ecoinfo/issues/55862012-04-16T18:54:00ZJing Taotao@nceas.ucsb.edu
<p>Here is an email from kepler user:</p>
<p>--------------------------------------------------------------<br />Running v2.3 on Mac OSX 10.7.3 Fairly new to Kepler.</p>
<p>I'm trying to use the EML 2 Dataset Actor to read in a local copy (in a folder on my laptop drive) of a sample metadata (.xml) file using the EML 2.1.0 schema and a simple 4-column data (.txt) file. I have checked the files using the <a class="external" href="http://knb.ecoinformatics.org/emlparser/">http://knb.ecoinformatics.org/emlparser/</a> site, and both were validated.</p>
<p>Two problems:<br />i) If I change either file the Actor doesn't keep up with the changes. It seems to revert to a cached version of the file as it was when I first specified it to the Actor (via the EML File: and Data File: fields in Configure Actor).<br />ii) I wondered about checking the "Check for latest version" checkbox. However doing this generates an error dialog with the message "null Please enter a new value:" I have to uncheck to stop the error.<br />----------------------------------------------------------------</p>
<p>So we may need a feature:<br />When the "Check for latest version" box is checked, Kepler will check local files as well.</p> Bug #5483 (New): Another Kepler GUI will nuke the ~/.kepler/cache generated by the kepler in work...https://projects.ecoinformatics.org/ecoinfo/issues/54832011-09-08T16:14:50ZJing Taotao@nceas.ucsb.edu
<p>The workflow run engine embeds a kepler at workflowrunengine/kepler. Now the workflow run engine runs the kepler by calling the API of the kepler.</p>
<p>I found an issue that if we start another kepler GUI in another location, e.g. ~/project/kepler, the kepler gui will nuke the ~/.kepler/cache directory even though they are in the same suite. This may cause a problem to run the workflow run engine. However, if we start the kepler gui from workflowrunengine/kepler, the kepler gui wouldn't nuke the cache directory generated by the run engine.</p> Bug #5474 (New): Make the eml actor on kepler handle multiple physical representations in an entityhttps://projects.ecoinformatics.org/ecoinfo/issues/54742011-08-19T16:17:49ZJing Taotao@nceas.ucsb.edu
<p>Wade Sheldon from GCE-LTER brought an question if the eml actor can handle mutiple physical representations in an entity.</p>
<p>I took a look at code and found kepler can't handle this correctly. In org.ecoinformatics.seek.datasource.eml.eml2.Eml200Parser class, we always use</p>
<p>physical/dataFormat/textFormat/simpleDelimited/collapseDelimiters, physical/distribution/online/url/@function and et al directly. And also we only get the value from the node which index is 0.</p>
<p>This will handle entity with one physical representation correctly. But it will failed when an entity has more than one physical representation.</p>
<p>For example, a dataTable has two physicals. The first one isn't textFormat and has a downloadable url. The second one is textFormat and has a downloadable url.</p>
<p>Kepler will download the first non-text data object and ignore the second text data object. And the worst case is that kepler will mismatch the non-text data object with the text format information from the second text data object.</p> Bug #5444 (In Progress): Kepler can't run workflow if two instances exist at same timehttps://projects.ecoinformatics.org/ecoinfo/issues/54442011-07-30T00:21:27ZJing Taotao@nceas.ucsb.edu
<p>Both vanilla and reporting suites (2.3) have problems. But the behaviors are different:<br />1. Vanilla kepler:</p>
<p>Start a kepler then start antoher one. The second one runs a workflow. Then close the first kepler. Finally close the second one, it shows the error:<br />java.sql.SQLException: Connection is broken: java.io.EOFException<br />at org.hsqldb.jdbc.Util.sqlException(Unknown Source)<br />at org.hsqldb.jdbc.jdbcStatement.fetchResult(Unknown Source)<br />at org.hsqldb.jdbc.jdbcStatement.execute(Unknown Source)<br />at org.kepler.util.sql.DatabaseType._executeSQL(DatabaseType.java:930)<br />at org.kepler.util.sql.HSQL.disconnect(HSQL.java:79)<br />at org.kepler.objectmanager.lsid.LSIDGenerator.closeDatabase(LSIDGenerator.java:400)<br />at org.kepler.module.core.Shutdown.shutdownModule(Shutdown.java:48)<br />at org.kepler.Kepler._initializeModules(Kepler.java:572)<br />at org.kepler.Kepler.access$100(Kepler.java:81)<br />at org.kepler.Kepler$Shutdown.shutdown(Kepler.java:663)<br />at org.kepler.util.ShutdownNotifier.shutdown(ShutdownNotifier.java:48)<br />at org.kepler.gui.KeplerGraphFrame.dispose(KeplerGraphFrame.java:1146)</p>
<p>2. Reporting kepler.<br />Two kepers are running. One runs a workflow and get an error:<br /><jing> ptolemy.kernel.util.IllegalActionException: Error recording workflow structure: Error connecting or initializing database.
{DB User Name=sa, Password=, DB Host=, DB Name=provenanceDB, DB Type=HSQL, DB Port=9002, DB Table Prefix=, JDBC URL=}<br />The database is already in use by another process: lockFile: org.hsqldb.persist.LockFile@aef9f24b[file =/home/tao/KeplerData/modules/provenance/db-2.3/provenanceDB.lck, exists=true, locked=false, valid=false, ] method: checkHeartbeat read: 2011-07-28 13:32:04.979 heartbeat - read: -8463 ms.<br />in .testWithReport.TOP Provenance Recorder<br />Because:<br />Error connecting or initializing database.
{DB User Name=sa, Password=, DB Host=, DB Name=provenanceDB, DB Type=HSQL, DB Port=9002, DB Table Prefix=, JDBC URL=}<br />The database is already in use by another process: lockFile: org.hsqldb.persist.LockFile@aef9f24b[file =/home/tao/KeplerData/modules/provenance/db-2.3/provenanceDB.lck, exists=true, locked=false, valid=false, ] method: checkHeartbeat read: 2011-07-28 13:32:04.979 heartbeat - read: -8463 ms.<br />at org.kepler.provenance.ProvenanceRecorder._recordWorkflowContents(ProvenanceRecorder.java:2618)<br />at org.kepler.provenance.ProvenanceRecorder.preinitialize(ProvenanceRecorder.java:583)<br />at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1682)<br />at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:930)<br />at ptolemy.actor.Manager.initialize(Manager.java:636)<br />at ptolemy.actor.Manager.execute(Manager.java:340)<br />at ptolemy.actor.Manager.run(Manager.java:1111)<br />at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1641)</p> Bug #5362 (New): Create a GUI so user can easily archive a senosr's data from a dataturbine to a ...https://projects.ecoinformatics.org/ecoinfo/issues/53622011-03-31T21:39:54ZJing Taotao@nceas.ucsb.eduBug #5339 (New): In Database Query actor, the output port will be string type if you choose the o...https://projects.ecoinformatics.org/ecoinfo/issues/53392011-03-04T02:05:33ZJing Taotao@nceas.ucsb.edu
<p>Derik and I found that the type of the output port is string even though we chose "record" as the output type.</p> Bug #5338 (New): In Database Query actor, the output behavior will be different if there is no re...https://projects.ecoinformatics.org/ecoinfo/issues/53382011-03-04T02:02:36ZJing Taotao@nceas.ucsb.edu
<p>If there is result set found and the output type is "array":<br />no token will be sent if you select "outputEachRowSeparately" in configuration panel;<br />no token will be send but a message "no match result for query ..." will be shown if you don't select "outputEachRowSeparately".</p>
<p>If there is result set found and the output type is "no metadata".<br />no token will be sent if you select "outputEachRowSeparately" in configuration panel;<br />A token ( I guess "/n") will be sent out if you don't select "outputEachRowSeparately".</p> Bug #5336 (New): If a user chooses "no metadata" as output format in Database Query actor, the qu...https://projects.ecoinformatics.org/ecoinfo/issues/53362011-03-04T01:45:15ZJing Taotao@nceas.ucsb.edu
<p>If user chooses the output type as "no metadata" (no column name will be shown in the result), and query looks like "select id, lastTime from sensors where id='sensor0', the result only shows:</p>
<pre><code>sensor0</code></pre>
<p>The lastTime column is missed even though the sensor0 does have a value at the lastTime column</p> Bug #5177 (New): Enhance displaying workflow in kepler server library skinhttps://projects.ecoinformatics.org/ecoinfo/issues/51772010-09-16T00:43:48ZJing Taotao@nceas.ucsb.edu
<p>This bug is the secondary stag of bug 5145.</p>
<p>Here are from matt:</p>
<p>If you are in the process of revamping this stylesheet and presentation, its<br />probably worthwhile to also consider improving the presentation style. Please<br />review some other sites that display workflows on the web, including:</p>
<p>MyExperiment:<br /> Workflow: <a class="external" href="http://www.myexperiment.org/workflows/23.html">http://www.myexperiment.org/workflows/23.html</a><br /> Resultset: <a class="external" href="http://www.myexperiment.org/tags/49.html?type=workflows">http://www.myexperiment.org/tags/49.html?type=workflows</a></p>
<p>CrowdLabs:<br /> Workflow: <a class="external" href="http://www.crowdlabs.org/vistrails/workflows/details/119/">http://www.crowdlabs.org/vistrails/workflows/details/119/</a></p> Bug #3291 (New): IPCC_ChangeNightlyBuildTest got an exceptionhttps://projects.ecoinformatics.org/ecoinfo/issues/32912008-05-09T21:57:31ZJing Taotao@nceas.ucsb.edu
<p>Running work-flow, demos/ENM/IPCC_Change_NightlyBuildTest.xml, got an exception. The supposed result is "true", but the result is not. So Nonstrict Test actor threw an exception.</p> Bug #3290 (New): DarwinCore_test workflow takes forever to downloading datahttps://projects.ecoinformatics.org/ecoinfo/issues/32902008-05-09T20:48:28ZJing Taotao@nceas.ucsb.edu
<p>DarwindCore actor in demos/ENM/DarwindCore_test.xml work-flow takes forever to downloading data (more than two hours) in mac. However, DarwinCore actor in demo/ENM/garpModel_ImageJ_withData.xml can download data in couple minutes. I deleted the cache before the both downloading.</p>
<p>I compared the end point of both actors, they are same. I have no idea one works but another one doesn't.</p>
<p>Can we remove the DarwindCord_test work-flow from the release?</p> Bug #3228 (New): Kepler need a central place to handle network disconnectionhttps://projects.ecoinformatics.org/ecoinfo/issues/32282008-04-16T23:21:06ZJing Taotao@nceas.ucsb.edu
<p>When we start kepler, if there is no network disconnection, kepler should have a decent way to handle it - for example, having a broken network sign (like Morpho does) and disabling the data search and other network relevant buttons. When network connection is found, those buttons will be enabled.</p>
<p>We need more thought here and any comment will be appreciated.</p> Bug #2230 (In Progress): EML actor doesn't handle footer line in data filehttps://projects.ecoinformatics.org/ecoinfo/issues/22302005-10-13T17:45:58ZJing Taotao@nceas.ucsb.edu
<p>Currently our delimiter reader only handle head line number and doesn't handle<br />foot line in data file. We need to support this feature.</p> Bug #2225 (In Progress): EML parser does not handle attribute list referencehttps://projects.ecoinformatics.org/ecoinfo/issues/22252005-10-10T22:08:25ZJing Taotao@nceas.ucsb.edu
<p>Currently, our eml parser in kepler couldn't handle attribute list reference.<br />And it couldn't handle entity reference either. We need to fix this bug.</p>