https://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-11-03T18:07:37ZEcoinformatics RedmineKepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191632011-11-03T18:07:37ZDaniel Crawldanielcrawl@gmail.com
<ul></ul><p>For the first bug: in my experience, changes to the actor metadata file do not appear in Kepler unless .kepler is removed.</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191642011-11-05T01:03:12ZChristopher Brookscxh@eecs.berkeley.edu
<ul></ul><p>Daniel suggested removing ~/.kepler to regenerate the docs. The docs are still empty for me after removing ~/.kepler.</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191652011-11-05T01:30:42ZDaniel Crawldanielcrawl@gmail.com
<ul></ul><p>The userLevelDocumentation property must be enclosed by the KeplerDocumentation property. I fixed this in RunCompositeActor.xml, and, after removing ~/.kepler, the documentation appears in the actor.</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191662011-11-05T20:15:16ZChristopher Brookscxh@eecs.berkeley.edu
<ul></ul><p>Thanks, I now get the Run Composite Actor documentation. There should be a bug report for the problem where userLevelDocumentation is not enclosed by the KeplerDocumentation. This seemed to fail silently, I was given no clue as to the problem.</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191672011-11-14T18:11:11ZDaniel Crawldanielcrawl@gmail.com
<ul></ul><p>I've updated the KARCacheManager to reload KARs if their modified time is different than when they were loaded into the cache. Now when an actor's documentation is updated in the XML file, the changes will appear in Kepler.</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191682011-11-14T18:32:32ZDaniel Crawldanielcrawl@gmail.com
<ul></ul><p>I've updated KeplerMetadataExtractor to display a warning when userLevelDocumentation is not enclosed by a KeplerDocumentation. If you set the log4j log level to debug, it also prints which actors are missing documentation:</p>
<p>Add Point To SVG is missing userLevelDocumentation and author documentation.<br />AlignmentEditor(Seaview) KeplerDocumentation is empty.<br />Anyof Parameter is missing userLevelDocumentation and author documentation.<br />Archive Counter is missing userLevelDocumentation and author documentation.<br />Array Append is missing userLevelDocumentation and author documentation.<br />ClustalWSeqAlign KeplerDocumentation is empty.<br />Copy From Node is missing userLevelDocumentation and author documentation.<br />Copy To Node is missing userLevelDocumentation and author documentation.<br />Create Expression From Query is missing userLevelDocumentation and author documentation.<br />Create Request From Result is missing userLevelDocumentation and author documentation.<br />Documentation is missing userLevelDocumentation and author documentation.<br />End Plan File is missing userLevelDocumentation and author documentation.<br />Execute On Node is missing userLevelDocumentation and author documentation.<br />GAMESS Plan File Generator is missing userLevelDocumentation and author documentation.<br />Histogram Plotter is missing userLevelDocumentation and author documentation.<br />IntRangeParameter is missing userLevelDocumentation and author documentation.<br />JRunCIPRes KeplerDocumentation is empty.<br />Logger is missing userLevelDocumentation and author documentation.<br />MappedLogger is missing userLevelDocumentation and author documentation.<br />MastOpalInput is missing KeplerDocumentation.<br />MemeOpalInput is missing userLevelDocumentation and author documentation.<br />On Error is missing userLevelDocumentation and author documentation.<br />Oneof Parameter is missing userLevelDocumentation and author documentation.<br />PAUPConsensusTrees KeplerDocumentation is empty.<br />Parameter is missing userLevelDocumentation and author documentation.<br />Random Parameter is missing userLevelDocumentation and author documentation.<br />Range Points Parameter is missing userLevelDocumentation and author documentation.<br />Range Step Parameter is missing userLevelDocumentation and author documentation.<br />SRB Add Metadata is missing userLevelDocumentation and author documentation.<br />SRB SPut is missing userLevelDocumentation and author documentation.<br />SRB Stream Put is missing userLevelDocumentation and author documentation.<br />SemanticTypeParameter is missing userLevelDocumentation and author documentation.<br />Sequence Scope is missing userLevelDocumentation and author documentation.<br />Server Execute is missing userLevelDocumentation and author documentation.<br />Single Parameter is missing userLevelDocumentation and author documentation.<br />Sleep is missing userLevelDocumentation and author documentation.<br />Start Plan File is missing userLevelDocumentation and author documentation.<br />Substitute is missing userLevelDocumentation and author documentation.<br />SyncOnTerminator is missing userLevelDocumentation and author documentation.<br />Temp Actor is missing userLevelDocumentation and author documentation.<br />Triggered Enum Item is missing userLevelDocumentation and author documentation.</p>
<p>I'm working on automatically generating the documentation for these using the Kepler doclet.</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191692011-11-14T18:37:07ZChristopher Brookscxh@eecs.berkeley.edu
<ul></ul><p>It is good that we are making progress on this, see also<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4909">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4909</a><br />Actor documentation: updates ignored, duplicate info, how to refer to other actors/models?</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191702012-08-23T00:18:44ZDaniel Crawldanielcrawl@gmail.com
<ul></ul><p>I added documentation based on the javadocs to:</p>
<p>AddPointToSVG.xml<br />AlignmentEditor_Seaview.xml<br />ArchiveCounter.xml<br />ArrayAppend.xml<br />ClustalWSeqAlign.xml<br />CreateExpressionFromQuery.xml<br />CreateRequestFromResult.xml<br />Documentation.xml<br />HistogramPlotter.xml<br />IntRangeParameter.xml<br />JRunCIPRes.xml<br />Logger.xml<br />MappedLogger.xml<br />MastOpalInput.xml<br />MemeOpalInput.xml<br />PAUPConsensusTrees.xml<br />Parameter.xml<br />SRBAddMetadata.xml<br />SRBSPut.xml<br />SRBStreamPut.xml<br />SemanticTypeParameter.xml<br />SequenceScope.xml<br />ServerExecute.xml<br />Sleep.xml<br />SyncOnTerminator.xml<br />TempActor.xml<br />TriggeredEnumItem.xml</p>
<p>The remaining actors missing documentation all appear to be composite actors in actors/src/org/resurgence/moml:</p>
<p>Anyof Parameter<br />Copy From Node<br />Copy To Node<br />End Plan File<br />Execute On Node<br />GAMESS Plan File Generator<br />On Error<br />Oneof<br />Random Parameter<br />Range Points Parameter<br />Range Step Parameter<br />Single Parameter<br />Start Plan File<br />Substitute</p>
<p>Christopher, what's left for this bug for 2.4?</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191712012-08-23T00:34:09ZChristopher Brookscxh@eecs.berkeley.edu
<ul></ul><p>Daniel, this bug looks fixed (thanks), so I'm closing it.</p> Kepler - Bug #5529: Documentation for some actors such as Run Composite Actor is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/5529?journal_id=191722013-03-27T21:30:47ZRedmine Admin
<ul></ul><p>Original Bugzilla ID was 5529</p>