Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-06T23:23:11ZEcoinformatics Redmine
Redmine Bug #5648 (Resolved): FileCopier code duplicationhttps://projects.ecoinformatics.org/ecoinfo/issues/56482012-08-06T23:23:11ZChristopher Brookscxh@eecs.berkeley.edu
<p>FileCopier:</p>
<p>./core/src/org/kepler/util/FileCopier.java - Fixed. Unused code which was removed.</p>
<p>./actors/src/org/sdm/spa/actors/transport/FileCopier.java - abstract base class extended by<br />./actors/src/org/sdm/spa/actors/transport/SftpCopier.java:public class SftpCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/ScpCopier.java:public class ScpCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/LocalFileCopier.java:public class LocalFileCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/SrmliteCopier.java:public class SrmliteCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/BbcpCopier.java:public class BbcpCopier extends FileCopier {</p>
<p>Fixed - Renamed this to FileCopierBase</p>
<p>The class that use FileCopier base is<br />actors/src/org/sdm/spa/actors/transport/FileCopierFactory.java<br />The Actor is:<br />actors/src/org/sdm/spa/actors/transport/GenericFileCopier.java</p>
<p>These two actors should be modified to call GenericFileCopier.java<br />./actors/src/org/resurgence/actor/FileCopier.java<br />./actors/src/org/kepler/actor/ssh/FileCopier.java</p> Bug #5642 (Resolved): Kepler should have access to the ShowTypes attributehttps://projects.ecoinformatics.org/ecoinfo/issues/56422012-07-20T17:09:54ZChristopher Brookscxh@eecs.berkeley.edu
<p>Edward added a ShowTypes attribute, that when dragged in to a model, annotates<br />the ports with the types.</p>
<p>In vergil, go to the left hand actor pane and do Utilities -> Analysis -> ShowTypes</p>
<p>In Kepler, Tools -> Instantiate Attribute<br />ptolemy.vergil.actor.lib.ShowTypes</p>
<p>Unfortunately, a green box without a name shows up, there is another bug for this:<br />bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: Text in attributes not rendered properly (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/4903">#4903</a></p> Bug #3575 (New): A representation of COMAD collections on the file-systemhttps://projects.ecoinformatics.org/ecoinfo/issues/35752008-10-27T21:33:47ZDaniel Zinndzinn@ucdavis.edu
<p>It would be useful if there were a representation of Collections in the file<br />system. In particular, I could imagine using directories to represent<br />collections (say named with a running number and the name of the<br />collection). Then we could use files to represent data items and<br />mata-data (for collections and data); For each data Token we could name<br />the file the same as the Type of the Token (with a leading running id),<br />and store a serialized version of the data token in it (which would be<br />easy for strings, for example). We could use the same file-name with a<br />suffix of, say, .METADATA:owner to store the metadata with the key owner<br />inside (possibly also with the type of the metadata in the string of the<br />filename).</p>
<p>This would not only make collections browse-able via standard<br />file-system tools, but since there exist distributed filesystems (such<br />as the hadoop filesystem) the size of these collections can easily scale<br />up to TBs of data.</p>
<p>This is somewhat similar to request <a class="issue tracker-1 status-1 priority-2 priority-default" title="Bug: Support for importing file contents automatically using CollectionSource (New)" href="https://projects.ecoinformatics.org/ecoinfo/issues/3573">#3573</a>, but aims more towards a general 'storage'-backend for COMAD 2 collections.</p>
<p>I am not proposing that some intermediary result should be represented as directories (though my request does not exclude this either). I am just requesting that besides the XML-representation of COMAD collections (that we currently have, right?) it would be good to have a representation that is file-system based. Similar to the XML representation, which is not materialized within a workflow run (ie, during the actors), the directory-representation need not to be materialized inside the workflow. Instead it should be a user-friendly way of browsing (and even creating) COMAD collections with ordinary file-manipulation tools. You can then copy or move content from one collection (=directory) to some other collection. This representation can then be used as inputs for workflows and can be an output format (to have a closed-loop system).</p>
<p>Besides gaining the power of simple file(system)-manipulation tools back for COMAD collections, this representation can be stored on a distributed file-system (ie hadoop fs) and the collection with the data can so easily hold terabytes of data.</p>
<p>What I am proposing are two actors, one that reads a (special) directory into a COMAD collection and one that can save any comad collection (stream) into a specially formated directory.</p> Bug #3234 (Resolved): IJMacro does not work in several demo workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/32342008-04-18T07:38:12ZSean Riddleswriddle@gmail.com
<p>Running on an installed version of Kepler on OS X.5, in several ENM workflows that try to use IJMacro to display an image, instead a dialog pops up that reports, "Unrecognized command: ASC TextReader."</p>
<p>Workflows in question:<br />ENM/GARP_*<br />ENM/garpModel*</p> Bug #3093 (Resolved): Unit test org.nddp.TestCollectionIOPort does not compilehttps://projects.ecoinformatics.org/ecoinfo/issues/30932008-01-23T00:57:33ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>The JUnit test org.nddp.TestCollectionIOPort does not compile, and has been renamed to TestCollectionIOPort.javaDISABLED in the repository.</p>
<p>The error message is:</p>
<p>org.nddp.TestCollectionIOPort.ComponentEntity_Local is not abstract and does not override abstract method removeInitializable(ptolemy.actor.Initializable) in ptolemy.actor.Initializable</p>
<p>I will try to fix this tomorrow, 1/23/2008.</p> Bug #3091 (Resolved): Warnings building org.nddp.DataTypeshttps://projects.ecoinformatics.org/ecoinfo/issues/30912008-01-23T00:31:08ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>Building Kepler yields two warnings with the message, "non-varargs call of varargs method with inexact argument type for last parameter". The offending code is in org.nddp.DataTypes.</p>
<p>I will try to fix this tomorrow, 1/23/2008.</p> Bug #2493 (Resolved): actor repository tracking bughttps://projects.ecoinformatics.org/ecoinfo/issues/24932006-07-18T21:42:18ZDan Higginshiggins@nceas.ucsb.edu
<p>The Kepler repository at <a class="external" href="http://library.kepler-project.org/">http://library.kepler-project.org/</a> currently has 52 components in it, but (nearly?) all are just copies of actors already built into Kepler. If downloaded and imported (using the menu item 'File/Import Archive (KAR)', one gets an error because the LSID is already in use (because the actor is already in Kepler). We need to remove any actors that are just duplicates.</p>
<p>Also, all files (KARs) downloaded from the repository seemed to be named just 'data' on download (at least on a Windows box). Download name should be more meaningful and should end with '.kar' since that is the file extention that Kepler is looking for to import the file.</p> Bug #2409 (Resolved): Display Name Not Showing for org.sdm.spa.Pause and org.sdm.spa.Stophttps://projects.ecoinformatics.org/ecoinfo/issues/24092006-04-11T17:18:10ZMatthew Brookebrooke@nceas.ucsb.edu
<p>org.sdm.spa.Pause and org.sdm.spa.Stop</p>
<p>When dragged to canvas, name ("Pause" or "Stop") does not show up. Right click on actor and select "Customize Name" - in this dialog, the "Show Name" checkbox is unchecked; however, if you check it and commit, you get an exception:</p>
<p>ptolemy.kernel.util.IllegalActionException: Cannot delete. This attribute is part of the class definition.<br /> in .all-actors-displayed-part1a.Pause._hideName<br /> at ptolemy.moml.MoMLParser._deleteProperty(MoMLParser.java:3955)<br /> at ptolemy.moml.MoMLParser.access$500(MoMLParser.java:199)<br /> at ptolemy.moml.MoMLParser$DeleteRequest.execute(MoMLParser.java:6280)<br /> at ptolemy.moml.MoMLParser._processPendingRequests(MoMLParser.java:5488)<br /> at ptolemy.moml.MoMLParser.endElement(MoMLParser.java:854)<br /> at com.microstar.xml.XmlParser.parseETag(XmlParser.java:1023)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1095)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)<br /> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:479)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:157)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:130)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1281)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1409)<br /> at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:270)<br /> at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:139)<br /> at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:685)<br /> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1618)<br /> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:907)<br /> at ptolemy.actor.gui.RenameConfigurer.apply(RenameConfigurer.java:165)<br /> at ptolemy.actor.gui.RenameDialog._handleClosing(RenameDialog.java:69)<br /> at ptolemy.gui.ComponentDialog$1.propertyChange(ComponentDialog.java:192)<br /> at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:333)<br /> at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:270)<br /> at java.awt.Component.firePropertyChange(Component.java:7225)<br /> at javax.swing.JOptionPane.setValue(JOptionPane.java:1896)<br /> at javax.swing.plaf.basic.BasicOptionPaneUI$ButtonActionListener.actionPerformed(BasicOptionPaneUI.java:1182)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)<br /> at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:234)<br /> at java.awt.Component.processMouseEvent(Component.java:5554)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)<br /> at java.awt.Component.processEvent(Component.java:5319)<br /> at java.awt.Container.processEvent(Container.java:2010)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4021)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2068)<br /> at java.awt.Component.dispatchEvent(Component.java:3869)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2054)<br /> at java.awt.Window.dispatchEventImpl(Window.java:1774)<br /> at java.awt.Component.dispatchEvent(Component.java:3869)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<br /> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:275)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:186)<br /> at java.awt.Dialog$1.run(Dialog.java:515)<br /> at java.awt.Dialog.show(Dialog.java:536)<br /> at java.awt.Component.show(Component.java:1300)<br /> at java.awt.Component.setVisible(Component.java:1253)<br /> at ptolemy.gui.ComponentDialog.<init>(ComponentDialog.java:233)<br /> at ptolemy.gui.ComponentDialog.<init>(ComponentDialog.java:101)<br /> at ptolemy.actor.gui.RenameDialog.<init>(RenameDialog.java:56)<br /> at ptolemy.vergil.kernel.RenameDialogFactory$1.actionPerformed(RenameDialogFactory.java:94)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)<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:334)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1041)<br /> at java.awt.Component.processMouseEvent(Component.java:5554)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)<br /> at java.awt.Component.processEvent(Component.java:5319)<br /> at java.awt.Container.processEvent(Container.java:2010)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4021)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2068)<br /> at java.awt.Component.dispatchEvent(Component.java:3869)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2054)<br /> at java.awt.Window.dispatchEventImpl(Window.java:1774)<br /> at java.awt.Component.dispatchEvent(Component.java:3869)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<br /> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:275)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)</p> Bug #2393 (New): Need ability to disable 'add port' to actors where not supportedhttps://projects.ecoinformatics.org/ecoinfo/issues/23932006-04-03T21:52:01ZDan Higginshiggins@nceas.ucsb.edu
<p>Currently one can 'add a port' to any actor even when that actor is not designed to look for new ports. This has confused some new users. It would be useful if there was a way to disable the add port button for individual actors (or enable it for only certain actors!)</p> Bug #2252 (Resolved): Need to add actors for aligning mulitiple DNA or protein sequenceshttps://projects.ecoinformatics.org/ecoinfo/issues/22522005-11-07T02:33:23ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>We need to wrap the ClustalW and Gblocks programs in collection-oriented actors.<br /> The aligned sequences output by these actors could then be fed into the actors<br />wrapping the Phylip package and used for inferring phylogenetic trees.</p> Bug #2249 (In Progress): Need to support a useful subset of PHYLIP (PHYlogeny Inference Package)https://projects.ecoinformatics.org/ecoinfo/issues/22492005-11-07T01:59:59ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>At present, actors wrap the following PHYLIP programs (but do not yet support<br />all features of these programs):</p>
<pre><code>consense, dnaml, dnamlk, dnapars, dnapenny, <br /> drawgram, pars, penny, proml, promlk, protpars</code></pre>
<p>At the very least, the following programs need to be wrapped by new actors and<br />their basic capabilities supported:</p>
<pre><code>dnadist, protdist, seqboot, fitch, kitsch, neighbor, factor, drawtree</code></pre> Bug #1697 (Resolved): Create a DarwinCore Actorhttps://projects.ecoinformatics.org/ecoinfo/issues/16972004-09-20T13:14:36ZRod Spearsrods@ku.edu
<p>After returning results from a DiGIR query we need to consolidate the results in<br />order to create the proper MetaData for each different endpoint that appeared.</p> Bug #1666 (Resolved): Create actor(s) for openModeller frameworkhttps://projects.ecoinformatics.org/ecoinfo/issues/16662004-09-01T05:16:45ZRicardo Pereirarpereira@ku.edu
<p>Need to create actors for openModeller Ecological Niche Modeling framework.</p>
<p>Potential actors to be created:</p>
<p>openModeller: Create Model<br />openModeller: Projection<br />openModeller: Sample</p>
<p>These actors will replace current GARP actors and correspondent C++ code in <br />Kepler.</p> Bug #1660 (Resolved): Add QueryBuilder to the Data Actorshttps://projects.ecoinformatics.org/ecoinfo/issues/16602004-08-23T18:38:08ZRod Spearsrods@ku.edu
<p>Need to add a query object to the Data Actors and be able to invoke the Query<br />Builder to make changes to it</p> Bug #1595 (Resolved): Create Advance Query Builder UIhttps://projects.ecoinformatics.org/ecoinfo/issues/15952004-06-08T11:56:05ZRod Spearsrods@ku.edu
<p>Create a UI to enabled a user to specifiy a query for an access actor (Query<br />Builder)</p>
<p>The QB will take as input:<br />1) Nothing<br />2) A kepler\src\org\ecoinformatics\seek\datasource object</p>
<p>The ouput:<br />A composite query object representing the query (with joins and where clause)</p>
<p>Rough Sketch:<br />The UI contain two panes:</p>
<p>1) The upper pane <br /> a) Shows all the tables defined in the database.<br /> b) The user will be able to D&D fields from one table to another to define<br /> foreign keys and/or table joins.</p>
<p>2) The lower pane will contain a tab control with two tabs<br /> a) The less advanced tab will enable a user to enter the defeinition of a<br /> where clause and all the items and their conditions will be grouped <br /> by either an "and" or an "or". The text will read "Must meet all of <br /> the conditions" or "Must meet at least one of the conditions" </p>
<pre><code>b) The advanced tab will enable a a user specify a much more complex, <br /> nested version of "ands" and "ors" This UI will look very close to the<br /> the Query Builder UI for the Ecogrid (See below)</code></pre>
<p>Description of UI for Advanced UI of the lower tab:<br /><AND><br /> <the condition goes here><br /> <OR><br /> <another condition goes here><br /> <another condition goes here><br /> </OR><br /></AND></p>