Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362005-11-16T18:18:23ZEcoinformatics Redmine
Redmine Bug #2277 (Resolved): Simplify Kar loadinghttps://projects.ecoinformatics.org/ecoinfo/issues/22772005-11-16T18:18:23ZKevin Rulandkruland@ku.edu
<p>For first release, simplify the kar loading process to operate on moml documents<br />only. Each moml file will describe a single actor.</p> Bug #2269 (Resolved): SVG - Small Icon (Actor Library Thumbnail)https://projects.ecoinformatics.org/ecoinfo/issues/22692005-11-11T20:05:32ZMatthew Brookebrooke@nceas.ucsb.edu
<p>getIcon() method in XMLIcon works, but its success seems to be linked to the odd<br />tree refreshing behavior described in bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: unexpected workflow components tree behavior (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1843">#1843</a>, which sends multiple calls to<br />getIcon().</p>
<p>When 1843 gets fixed, we may be able to make getIcon() more efficient/intuitive,<br />and this may in turn save some memory usage (see bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: SVG - Memory Usage (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2267">#2267</a>). Another way to save<br />memory and improve app response time is to assign gif/png thumbnail icons to the<br />actors, since these are already available in docs/dev/usability/graphics/ - it<br />seems like an unnecessary use of resources to use Batik to render these thumbnails.</p> Bug #2268 (Resolved): SVG - Backward Compatibilityhttps://projects.ecoinformatics.org/ecoinfo/issues/22682005-11-11T19:59:38ZMatthew Brookebrooke@nceas.ucsb.edu
<p>- Need to add code so old SVG icons are translated to have their origin at the<br />top-left corner. They are currently cropped when displayed in batik, because<br />Ptolemy's default origin for svg components is at the center of each actor icon,<br />whereas the svg/batik standard is to have the origin at top-left.</p>
<p>Another possibility (and one which would temporarily help with the memory usage<br />problems - see bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: SVG - Memory Usage (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2267">#2267</a>) would be to continue using PTII's SVG rendering for<br />the old "simple" svg icons, and use batik only for the new icons.</p> Bug #2266 (Resolved): SVG - Assigning Iconshttps://projects.ecoinformatics.org/ecoinfo/issues/22662005-11-11T19:49:48ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Icons can be assigned in actor moml, or can be assigned in the actor's java<br />code. Assigning in moml means icons will show up for newly-created workflows,<br />but <strong>not</strong> for old workflows. [Note that some actors can't be set via moml (eg<br />EML200 datasource), so would need to add some to java code anyway]</p>
<p>Adding icon paths directly to the actors' java code (note that existing svg<br />icons are currently defined in java code) means icons show up for all actors, in<br />new <strong>and</strong> old workflows. Could move actual actor->svg icon mappings into a<br />separate settings file? Or would this cause too much indirection and add<br />complication?</p>
<hr />
<p>conf call of 11/10/05 - decided to put assignments in actor code, with actual<br />mappings in a separate config file to allow for easy changes</p> Bug #2255 (Resolved): Simple Composite Actor cannot be dragged onto displayhttps://projects.ecoinformatics.org/ecoinfo/issues/22552005-11-08T17:29:37ZDan Higginshiggins@nceas.ucsb.edu
<p>The simple, empty 'Composite Actor' does not appear in the actor tree because it<br />has been 'commented out' in the actorList.moml file. Uncommenting it makes it<br />appear in the actor tree, but then dragging it to the right to place it in a<br />workflow creates an error! ("Property is not an instance of Attribute...").</p>
<p>Being able to simply create a Composite Actor by dragging it to the work area<br />seems to be fairly important.</p> Bug #2253 (Resolved): ENM Workflows errors on newer, faster computerhttps://projects.ecoinformatics.org/ecoinfo/issues/22532005-11-07T17:32:51ZDan Higginshiggins@nceas.ucsb.edu
<p>Errors are occurring in 'SingleSpecies_BestRuleSet_Aug2005 ENM workflow on new,<br />faster computer (Optiiplex GX620 - 3GHz dual core - Win XP) that do not occur<br />when same workflow is run on older, slower machine (null pointer error most of<br />time). Error seems to occur at end of GARP run; perhaps a file is not ready?</p>
<p>Possible threading problem?</p> Bug #2243 (Resolved): bug in inverse distance interpolation in Grid Rescaling actorhttps://projects.ecoinformatics.org/ecoinfo/issues/22432005-11-04T17:22:58ZDan Higginshiggins@nceas.ucsb.edu
<p>An attempt to smooth the IDW interpolation near NO_DATA edges of a grid has<br />resulted in errors in interpolation (that are clearly visible as a 'waffle' type<br />background in images).</p>
<p>Reason for this bug is currenly unclear. Needs to be fixed for use in ENM workflow.</p> Bug #2235 (Resolved): Search text-field only 1 character wide on Mac OS Xhttps://projects.ecoinformatics.org/ecoinfo/issues/22352005-10-25T22:41:14ZMatthew Brookebrooke@nceas.ucsb.edu
<p>On the left-hand side of the Kelper UI, the text field in which the user types<br />search terms is only 1 character wide when displayed on Mac OS X - this is<br />because the buttons are much wider than those on windows/linux</p> Bug #2233 (Resolved): Name duplication exception with KAR fileshttps://projects.ecoinformatics.org/ecoinfo/issues/22332005-10-19T22:07:28ZEfrat Jaegerjaeger@ecoinformatics.org
<p>The new kar system throws a name duplication exception when two kars <br />implemented by (perhaps completely) different actors share the same name. We'd <br />like to have both actors, so we probably need some kar's naming conventions.</p> Bug #2141 (Resolved): resultset cache expiration problemhttps://projects.ecoinformatics.org/ecoinfo/issues/21412005-07-05T21:31:30ZChad Berkleyberkley@nceas.ucsb.edu
<p>The cache needs to be fixed so that resultsets expire and are purged according<br />to a set policy. This was discussed at the 05 june kepler meeting. efrat and<br />jing agreed to fix it.</p> Bug #2108 (Resolved): changes to simple searchhttps://projects.ecoinformatics.org/ecoinfo/issues/21082005-06-10T17:57:54ZLaura Downeyldowney@lternet.edu
<p>1) remove "text" and "concept" checkboxes<br />2) change "go" to "search" <br />3) make "enter" key execute "search" not "reset"</p> Bug #2025 (Resolved): provide workflow and results in some publishable formathttps://projects.ecoinformatics.org/ecoinfo/issues/20252005-03-11T20:45:26ZLaura Downeyldowney@lternet.edu
<p>provide a workflow "package" of the workflow and its results in a publishable <br />format -- this would be more extensive than just the natural language summary <br />of a workflow referred to in bug 2024</p> Bug #2008 (Resolved): Provide real-time feedback for workflow progress as a defaulthttps://projects.ecoinformatics.org/ecoinfo/issues/20082005-03-11T18:41:22ZDan Higginshiggins@nceas.ucsb.edu
<p>suggested by Laura Downey. This can currently be done in SDF workflows by using<br />the 'Animate Execution' command under the Debug menu, but is not the default and<br />does't work under other Directors.</p> Bug #1882 (Resolved): Investigate UI Changeshttps://projects.ecoinformatics.org/ecoinfo/issues/18822005-01-20T17:20:25ZRod Spearsrods@ku.edu
<p>Work with Laura to investigate the level of effort needed to make the UI changes<br />to Kepler (most of these changes impact Ptolemy)</p>
<p>For example:<br />Changing the Context Menu (right click)<br />Changing the color schema<br />Localizing all the strings<br />Adding dropdown lists for port types<br />Better layout of dialogs</p> Bug #1851 (Resolved): save atomic and composite actors in the new actor libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/18512005-01-03T18:19:44ZWibke Sudholtwibke@oci.unizh.ch
<p>Cutted and pasted from email conversation:</p>
<p>On 03.01.2005 18:34, "Chad Berkley" <<a class="email" href="mailto:berkley@nceas.ucsb.edu">berkley@nceas.ucsb.edu</a>> wrote:</p>
<blockquote>
<p>Hi Shawn, Ilkay and Wibke,</p>
<p>This is probably our problem. There are several problems like this that <br />i've been finding as i've been working with our newly re-worked actor <br />library system. The best thing to do at this point is to enter a bug <br />and we can prioritize it and hopefully work on it at the kepler meeting <br />at the end of the month. I think there are several other bugs like this <br />so maybe we can fix them all at the same time.</p>
<p>chad</p>
<p>Shawn Bowers wrote:</p>
<blockquote>
<p>I'm not really sure what is causing your problem, but the actor library <br />uses the file basicKeplerActorLibrary.xml and not basicKeplerLibrary.xml.</p>
<p>This file is basically just wrapped by a <group> without any additional <br />"wrapper" (i.e., the UserLibrary stuff).</p>
<p>Shawn</p>
<p>Ilkay Altintas wrote:</p>
<blockquote>
<p>Hi Chad and Shawn,</p>
<p>Wibke had some problems with the cloning of the composite actors to <br />the actor library.<br />All the details are given below. I thought you guys would help her <br />better than me.</p>
<p>I tried the same thing that she is trying to do under the regular PTII <br />and it seems to work.<br />Please let me or her (cce'd) know if it is something we are missing or <br />unaware.</p>
<p>Wibke: The explanation below is great. Thanks so much for sending it.</p>
<p>Thanks everybody,<br />-ilkay</p>
<p>Begin forwarded message:</p>
<p>*From: *Wibke Sudholt <<a class="email" href="mailto:Wibke.Sudholt@web.de">Wibke.Sudholt@web.de</a>><br />*Date: *December 20, 2004 12:41:30 AM PST<br />*To: *Ilkay Altintas <<a class="email" href="mailto:altintas@sdsc.edu">altintas@sdsc.edu</a>><br />*Subject: Reuse of composite actors again
*<br />Hi Ilkay,</p>
<p>I think the problem with the reuse of composite actors is a problem<br />of the<br />new actor tree/ontology layout in Kepler.</p>
<p>According to the Ptolemy II documentation</p>
<p>(<a class="external" href="http://ptolemy.eecs.berkeley.edu/ptolemyII/ptIIlatest/ptII4.0.1/doc/design/">http://ptolemy.eecs.berkeley.edu/ptolemyII/ptIIlatest/ptII4.0.1/doc/design/</a></p>
<p>usingVergil/index.htm), things should basically work as described <br />in my<br />previous email. For example, the user library may look like this<br />(see also<br /><a class="external" href="http://ptolemy.eecs.berkeley.edu/~cxh/ptpub/addinganactor.htm">http://ptolemy.eecs.berkeley.edu/~cxh/ptpub/addinganactor.htm</a>):</p>
<p><entity name="UserLibrary" class="ptolemy.moml.EntityLibrary"><br /><configure><br /><group><br /><entity name="CompositeActor" class="myActors.CompositeActor"/><br /></group><br /></configure><br /></entity></p>
<p>So, the library is processed by ptolemy.moml.EntityLibrary via a<br />configure<br />group. This according to the documentation suppresses evaluation of<br />the MoML<br />commands as far as I understand. Thus when using<br />myActors.CompositeActor by<br />dragging & dropping onto the workspace, the MoML content under<br />entity is<br />used in the workflow exactly as it is put in the library.</p>
<p>In contrast, in Kepler the library basicKeplerLibrary.xml in the <br />Kepler<br />configs dir basically looks like this:</p>
<p><entity name="actor library" class="ptolemy.kernel.CompositeEntity"><br /><group><br />...<br /></group><br /></entity></p>
<p>In the middle (...) entities are imported via external files.<br />Differences<br />are that Kepler (1) uses the master class<br />ptolemy.kernel.CompositeEntity and<br />(2) directly implements the MoML entities, not via configure. As far<br />as I<br />understand, this does not suppress the evaluation of the MoML while<br />dragging<br />& dropping onto the workspace. In my case (see below) this leads <br />to the<br />source link being resolved and consequently the sub-entities of the<br />composite actor appearing two times in the workflow (one time via<br />the source<br />link copied and one time directly after resolving the link). This <br />might<br />perhaps explain the problems I observe when trying to include <br />composite<br />actor classes into the Kepler actor tree as described in my previous<br />email.</p>
<p>This is as far as I could find out up to now. I am of course not<br />really sure<br />if this is the reason for the problems or if I misunderstand<br />something here.<br />But I would be very happy if you could clarify this for me, since<br />you are<br />the much better Kepler expert than I am :-) and I am really stuck <br />here<br />currently ...</p>
<p>Thanks a lot,</p>
<p>Wibke</p>
<hr />
<p>Hi Ilkay,</p>
<p>I think I finally found a possibility to reuse/link composite actors.</p>
<p>One has to include something like the following into the xml file <br />which<br />describes the library for the actor tree:</p>
<p><entity class="resurgence.ClassTest" name="Class Test" <br />source="ptolemy/configs/kepler/resurgence/ClassTest.xml"><br /><property class="org.ecoinformatics.seek.util.NamedObjId" <br />name="entityId" value="urn:lsid:ecoinformatics.org:kepler.1302.1"/><br /></entity></p>
<p>The "source" attribute makes that the class MoML file (here<br />"ptolemy/configs/kepler/resurgence/ClassTest.xml") is reloaded each<br />time I<br />use a workflow which uses the entity.</p>
<p>To make changes in the classes work, one has to recompile<br />kepler-configs.jar, however.</p>
<p>Unfortunately, there are still problems with this setup. First of <br />all,<br />somehow a workflow generated on the workspace does not only get the<br />"entity" <br />entry from above, but also the contents of the ClassTest.xml file<br />included<br />(although it is still linked to this file, too, and the link works <br />e.g.<br />after changes and when looking inside a composite actor). Second,<br />whenever I<br />use ports and links etc. inside the class and not only just <br />entities, I<br />cannot dragg&dropp the actor to the workspace anymore and the<br />program hangs.<br />To me this actually looks like this might even be a bug in Ptolemy<br />or Kepler<br />...</p>
<p>Do you perhaps know how to solve this or could you forward this to a<br />person<br />who might know?</p>
<p>Thanks a lot,</p>
<p>Wibke</p>
</blockquote></blockquote></blockquote>