Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362005-07-05T21:14:02ZEcoinformatics Redmine
Redmine Bug #2137 (Resolved): create a docbook format for WF documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/21372005-07-05T21:14:02ZChad Berkleyberkley@nceas.ucsb.edu
<p>we need a docbook type format for workflow documentation. We agreed to look<br />into this at the june 05 kepler meeting. Ilkay agreed to take the lead.</p> Bug #2044 (Resolved): R actor for means and error by grouphttps://projects.ecoinformatics.org/ecoinfo/issues/20442005-03-11T23:37:40ZMatt Jonesjones@nceas.ucsb.edu
<p>This bug is to create an actor that wraps an R script (using the generic R actor<br />described in bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: need R actor (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1342">#1342</a>) for calculating the mean, standard deviation, and<br />standard error of a numeric variable that is passed into the script. Optionally<br />the stats should be calculated using a grouping variable (by group), with one<br />mean/std/se for each group.</p>
<p>There are two inputs:<br /> 1) dataValue (type double)<br /> 2) group (type string)</p>
<p>The actor will accululate all data passed in as a series of {dataValue, group}<br />tuples and pass this along to R to calculate the mean, stdev, and stderr by<br />group. If group is not present then the tuples will be {dataValue}. When the R<br />script is finished, a matrix of {group, mean, stdev, stderr} will be passed back<br />to the R actor and then emitted on the output port. So for N tokens that come<br />in on the input port the actor will output on 1 token on the output port after<br />all input data has been received (this is a grouping operation).</p> Bug #2010 (Resolved): Provide Clear/Reset for Searchhttps://projects.ecoinformatics.org/ecoinfo/issues/20102005-03-11T18:44:59ZDan Higginshiggins@nceas.ucsb.edu
<p>Suggested by Laura Downey<br />Already in Actor Search, but not implemented in Data search</p> Bug #1990 (Resolved): DataType of EML for KEPLERhttps://projects.ecoinformatics.org/ecoinfo/issues/19902005-02-26T02:10:20ZJing Taotao@nceas.ucsb.edu
<p>The Datatype really should be determined in EML from the measurementScale and<br />domain (numericDomain and nonNumericDomain). Using the storage type was<br />a hack that we kept in from our earlier Monarch code -- its very<br />unreliable, and is optional, which is why we at times have trouble. I<br />think I wrote about this in a bug for Kepler, but I can't find it.</p>
<p>The default Ptolemy types are fairly coarse grained, so we should get<br />fairly far by something simple:</p>
<p>MeasurementScale numberType Type<br />nominal N/A string<br />ordinal N/A string<br />interval/ratio natural int or long (depending on bounds)<br />interval/ratio whole int or long (depending on bounds)<br />interval/ratio integer int or long (depending on bounds)<br />interval/ratio real double<br />datetime ?</p>
<p>In the above, you can use bounds and precision to help fine tune which<br />of the numeric types to use.</p>
<p>In implementing this, its probably best to separate out the type<br />inference code from the rest as much as possible -- a separate method at<br /> a minimum, a separate class possibly. Keep in mind that this code is<br />probably going to be somewhat related to semantic type checking that<br />Shawn is working on.</p> Bug #1904 (Resolved): Nimrod implementation and templateshttps://projects.ecoinformatics.org/ecoinfo/issues/19042005-01-21T19:18:46ZIlkay Altintasaltintas@sdsc.edu
<p>Design (semi-)native Nimrod actors and/or use the remote Nimrod portal. Create<br />reusable patterns/templates for Nimrod based distributed execution.</p> Bug #1903 (Resolved): Wrappers to access ADN metadatahttps://projects.ecoinformatics.org/ecoinfo/issues/19032005-01-21T19:18:23ZEfrat Jaegerjaeger@ecoinformatics.orgBug #1885 (Resolved): Create new DataRelationsManagerhttps://projects.ecoinformatics.org/ecoinfo/issues/18852005-01-20T18:03:45ZRod Spearsrods@ku.edu
<p>This sits above the CacheManager and manages data that has been transformed<br />(loss less). This enables actors to asks the DataRealtionsManager (DRM) for data<br />but if there is data that has already been transofrmed then it will return that<br />instead so the actor can skip the transformation</p> Bug #1766 (Resolved): Error with Ecogrid searches for JVM 1.4.2_05 and _06https://projects.ecoinformatics.org/ecoinfo/issues/17662004-11-09T16:27:24ZDan Higginshiggins@nceas.ucsb.edu
<p>There is an error which occurs on Windows and Macs running JVM 1.4.2_05 and _06.<br />Error message is shown below. It occurs when searching the ecogrid with an empty<br />cache. Works OK for 1.4.1_04 and on all versions of Linux</p>
<pre><code>[java] The service type from configure file is EcoGridQueryInterface<br /> [java] The value of serviceName is KU Digir EcoGrid QueryInterface<br /> [java] The value of serviceType is EcoGridQueryInterface<br /> [java] The value of endPoint is <a class="external" href="http://kuecogrid.ittc.ku.edu:8080/ogsa/serv">http://kuecogrid.ittc.ku.edu:8080/ogsa/serv</a><br />ices/org/ecoinformatics/ecogrid/EcoGridQueryInterfaceLevelOneService<br /> [java] The value of namespace is <a class="external" href="http://digir.net/schema/conceptual/darwin/">http://digir.net/schema/conceptual/darwin/</a><br />full/2001/1.0<br /> [java] The value of label is Darwin Core 1.0<br /> [java] The namespace for this document type is <a class="external" href="http://digir.net/schema/conc">http://digir.net/schema/conc</a><br />eptual/darwin/full/2001/1.0<br /> [java] The label for this doucment type is Darwin Core 1.0<br /> [java] The metadata specification class name is org.ecoinformatics.seek.dat<br />asource.darwincore.DarwinCoreMetaDataSpecification<br /> [java] read service KU Digir EcoGrid QueryInterface from config file to vec<br />tor<br /> [java] java.lang.IllegalAccessError: tried to access field org.apache.xpath<br />.compiler.FunctionTable.m_functions from class org.apache.xml.security.Init<br /> [java] at org.apache.xml.security.Init.init(Unknown Source)<br /> [java] at org.globus.ogsa.impl.security.authentication.wssec.WSSecurity<br />Engine.&lt;clinit&gt;(WSSecurityEngine.java:55)<br /> [java] at org.globus.ogsa.impl.security.authentication.wssec.WSSecurity<br />ClientHandler.handleResponse(WSSecurityClientHandler.java:51)<br /> [java] at org.apache.axis.handlers.HandlerChainImpl.handleResponse(Hand<br />lerChainImpl.java:153)<br /> [java] at org.apache.axis.handlers.JAXRPCHandler.invoke(JAXRPCHandler.j<br />ava:84)<br /> [java] at org.globus.ogsa.utils.JAXRPCHandler.invoke(JAXRPCHandler.java<br />:16)<br /> [java] at org.apache.axis.strategies.InvocationStrategy.visit(Invocatio<br />nStrategy.java:71)<br /> [java] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:150)<br /> [java] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:120)<br /> [java] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:193)</code></pre>
<pre><code>[java] at org.apache.axis.client.Call.invokeEngine(Call.java:2564)<br /> [java] at org.apache.axis.client.Call.invoke(Call.java:2553)<br /> [java] at org.apache.axis.client.Call.invoke(Call.java:2248)<br /> [java] at org.apache.axis.client.Call.invoke(Call.java:2171)<br /> [java] at org.apache.axis.client.Call.invoke(Call.java:1691)<br /> [java] at org.ecoinformatics.ecogrid.stub.bindings.EcoGridQueryLevelOne<br />ServiceSOAPBindingStub.get(EcoGridQueryLevelOneServiceSOAPBindingStub.java:846)<br /> [java] at org.ecoinformatics.ecogrid.client.EcogridQueryClient.get(Ecog<br />ridQueryClient.java:297)<br /> [java] at org.ecoinformatics.seek.datasource.EcogridMetaDataCacheItem.d<br />oWork(EcogridMetaDataCacheItem.java:90)<br /> [java] at org.ecoinformatics.seek.datasource.DataCacheItem.run(DataCach<br />eItem.java:482)<br /> [java] at java.lang.Thread.run(Thread.java:534)</code></pre> Bug #1751 (Resolved): new mailing lists: kepler-users, kepler-voteshttps://projects.ecoinformatics.org/ecoinfo/issues/17512004-10-27T13:58:48ZBertram Ludaescherludaesch@sdsc.edu
<p>As the Kepler releases reach beta level (or better) it is important to discuss<br />end user requests, issues etc. One mailing list doesn't fit all, hence the<br />suggestion to separate out different ones:</p>
<p>- kepler-dev: same as now<br />- kepler-user(s?): questions, bug reports from end users, announcement of new<br />releases, maybe a monthly FAQ posting, etc<br />- kepler-votes: for Kepler members to vote on new members, technical issues etc</p>
<p>apropos VOTE: if you can (November 2nd) make use of it!!</p>
<p>Bertram</p> Bug #1747 (Resolved): provide display of full metadata for EML200DataSource actorshttps://projects.ecoinformatics.org/ecoinfo/issues/17472004-10-27T09:46:47ZMatt Jonesjones@nceas.ucsb.edu
<p>Current EML data source actors only display their title. This is not enough<br />information to evaluate and use a data set. Need to display the full EML record<br />on request.</p> Bug #1717 (Resolved): EML200 data source throws error on 'Look Inside'https://projects.ecoinformatics.org/ecoinfo/issues/17172004-10-13T21:37:06ZMatt Jonesjones@nceas.ucsb.edu
<p>After dragging an EML200 data source from the result list window to the canvas,<br />if one clicks on 'Look Inside' to configure it, it throws an exception. This<br />does not happen with the EML200 Simple Plot Example -- but happens consistently<br />with some other data packages. Exception is pasted below.</p>
<p>Steps to reproduce:</p>
<p>1) Open kepler and launch EML2 Simple plot workflow<br />2) Click on data tab, search for 'mollusc'<br />3) Choose the first of the GCE mollusc data package and drag to canvas<br />4) Right-click and choose 'Look Inside'</p>
<p>The error generated is:<br />ptolemy.kernel.util.IllegalActionException: Cannot graphically edit a model that<br />is not a CompositeEntity. Model is a<br />org.ecoinformatics.seek.datasource.eml.eml2.Eml200DataSource
{.eml-simple-plot-new.Mollusc population abundance monitoring: Fall 2001<br />mid-marsh and creekbank infaunal and epifaunal mollusc abundance based on<br />collections from GCE marsh, monitoring sites 1-}<br /> in .configuration.directory.effigy.Mollusc population abundance monitoring:<br />Fall 2001 mid-marsh and creekbank infaunal and epifaunal mollusc abundance based<br />on collections from GCE marsh, monitoring sites 1-.graphTableau<br /> at ptolemy.vergil.actor.ActorGraphTableau.<init>(ActorGraphTableau.java:98)<br /> at<br />ptolemy.vergil.actor.ActorGraphTableau$Factory.createTableau(ActorGraphTableau.java:162)<br /> at<br />ptolemy.actor.gui.PtolemyTableauFactory.createTableau(PtolemyTableauFactory.java:98)<br /> at ptolemy.actor.gui.TableauFactory.createTableau(TableauFactory.java:122)<br /> at ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java:193)<br /> at ptolemy.actor.gui.Configuration._openModel(Configuration.java:672)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:458)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:416)<br /> at<br />ptolemy.vergil.actor.ActorController$LookInsideAction.actionPerformed(ActorController.java:632)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1786)<br /> at<br />javax.swing.AbstractButton$ForwardActionEvents.actionPerformed(AbstractButton.java:1839)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:289)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1113)<br /> at<br />javax.swing.plaf.basic.BasicMenuItemUI$MouseInputHandler.mouseReleased(BasicMenuItemUI.java:943)<br /> at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:231)<br /> at java.awt.Component.processMouseEvent(Component.java:5100)<br /> at java.awt.Component.processEvent(Component.java:4897)<br /> at java.awt.Container.processEvent(Container.java:1569)<br /> at java.awt.Component.dispatchEventImpl(Component.java:3615)<br /> at java.awt.Container.dispatchEventImpl(Container.java:1627)<br /> at java.awt.Component.dispatchEvent(Component.java:3477)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:3483)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3198)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3128)<br /> at java.awt.Container.dispatchEventImpl(Container.java:1613)<br /> at java.awt.Window.dispatchEventImpl(Window.java:1606)<br /> at java.awt.Component.dispatchEvent(Component.java:3477)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:456)<br /> at<br />java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:201)<br /> at<br />java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:145)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:137)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:100)</p> Bug #1544 (Resolved): complete web service actorhttps://projects.ecoinformatics.org/ecoinfo/issues/15442004-04-30T17:45:55ZMatt Jonesjones@nceas.ucsb.edu
<p>Fix web service actor code --> Ilkay, Chad</p>
<p>This involves completing the code for a wider variety of data types, and making<br />sure that we support arrays.</p>
<p>1) New architecture for the class<br />2) Multiple output<br />3) Use java APIs<br />4) Add additional type support --> To support arrays of {int, short, long,<br />string, double, float, boolean}; Date</p> Bug #1342 (Resolved): need R actorhttps://projects.ecoinformatics.org/ecoinfo/issues/13422004-02-10T16:56:48ZChad Berkleyberkley@nceas.ucsb.edu
<p>create an actor to execute R jobs via kepler. Later, establish a GridService<br />that can handle this for us.</p> Bug #1338 (Resolved): find GIS system for inclusion in keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/13382004-02-09T19:14:52ZChad Berkleyberkley@nceas.ucsb.edu
<p>need to look at the various proposed solutions for GIS integration into Kepler.<br /> The possibilities that I've heard so far are GDAL and GRASS. It has also been<br />mentioned that the more basic GIS functionality could probably be implemented in<br />java or with a ptolemy pipeline using existing actors.</p> Bug #1332 (Resolved): GARP improvements and further implemenationhttps://projects.ecoinformatics.org/ecoinfo/issues/13322004-02-09T16:30:40ZChad Berkleyberkley@nceas.ucsb.edu
<p>The GARP pipeline needs to be extended to include the entire workflow from start<br />to finish. This has been prototyped but not implemented. also need to modify<br />the garp actors so that the inputs and outputs are more intuitive and use<br />streams instead of filenames.</p>
<p>expose garp params<br />(look at desktop garp)<br />------------------<br />runs<br />convergence limit<br />max iterations</p>
<p>--develop xml schema for the internal garp data rep. (cellset and ruleset xml files)<br />--get dave's and ricardo's garp code integrated with the kepler garp code (use a<br />single repository)<br />--standardize IO file format</p>