Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-08-21T20:27:56ZEcoinformatics Redmine
Redmine Kepler - Bug #6588 (New): R actor does not have error for missing outputhttps://projects.ecoinformatics.org/ecoinfo/issues/65882014-08-21T20:27:56ZDaniel Crawldanielcrawl@gmail.com
<p>If the R actor has an output port "x", but the script does not assign a value to a variable "x", then the actor should report an error. Currently, the actor successfully runs but does not write a token to the output port.</p> Kepler - Feature #6575 (New): reference parameters in R actor's scripthttps://projects.ecoinformatics.org/ecoinfo/issues/65752014-07-09T21:40:18ZDaniel Crawldanielcrawl@gmail.com
<p>It would be nice if the script in the R actor could reference parameters that were added to the R actor. Currently the R actor only converts tokens read on input ports to the R script.</p> EML - Feature #6079 (New): Support JSON or XML output from emlparserhttps://projects.ecoinformatics.org/ecoinfo/issues/60792013-09-06T18:12:45Zben leinfelderleinfelder@nceas.ucsb.edu
<p>The online parser servlet returns HTML, but there has been a request to support alternate output formats for programatic interactions.</p>
<p>Matt's proposed schema<br /><pre>
<!ELEMENT response (validation+)>
<!ELEMENT validation (message*)>
<!ATTLIST validation type (#PCDATA) #REQUIRED>
<!ATTLIST validation status (passed | failed) #REQUIRED>
<!ELEMENT message (#PCDATA)>
</pre></p>
<p>and example:</p>
<pre>
<response>
<validation type="emlparse" status="failed">
<message>Missing key for reference to node "154A12"</message>
<message>Missing key for reference to node "26A467"</message>
</validation>
<validation type="saxparse" status="passed" />
</response>
</pre> Kepler - Bug #5590 (New): RExpression forces pdf if 'automatically show graphics' is checkedhttps://projects.ecoinformatics.org/ecoinfo/issues/55902012-04-26T01:34:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Look into this forced format change side-effect which is confusing to a user. If you select e.g. png, and 'auto show..', you get a pdf.</p> FIRST - Bug #5053 (New): Attempt to download either yields empty file or throws an error (Bespin)https://projects.ecoinformatics.org/ecoinfo/issues/50532010-06-18T12:22:13ZSandeep Namilikondasandeep.namilikonda@gmail.com
<p>2007F_BS111_Exam3 (moyerbrailean.619.14)</p>
<p>Assessment has 50 items and displays all metadata on the website.<br />But, any attempt to download it seems to fail.<br />For example, with one metadata item chosen to be downloaded, a download<br />results in an empty .csv file to be returned.<br />When I increased this number, to say 10, then attempt to download <br />transpose or non-transpose resulted in the following error:</p>
<p>HTTP Status 500 -</p>
<p>type Exception report</p>
<p>message</p>
<p>description The server encountered an internal error () that prevented it from fulfilling this request.</p>
<p>exception</p>
<p>org.apache.jasper.JasperException: -1<br /> org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:460)<br /> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:373)<br /> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)<br /> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)<br /> javax.servlet.http.HttpServlet.service(HttpServlet.java:802)<br /> org.vfny.geoserver.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:122)<br />root cause</p>
<p>java.lang.ArrayIndexOutOfBoundsException: -1<br /> java.util.ArrayList.remove(ArrayList.java:392)<br /> org.apache.jsp.style.skins.first.download_jsp.transpose(download_jsp.java:335)<br /> org.apache.jsp.style.skins.first.download_jsp.handleDataquery(download_jsp.java:483)<br /> org.apache.jsp.style.skins.first.download_jsp._jspService(download_jsp.java:563)<br /> org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)<br /> javax.servlet.http.HttpServlet.service(HttpServlet.java:802)<br /> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)<br /> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)<br /> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)<br /> javax.servlet.http.HttpServlet.service(HttpServlet.java:802)<br /> org.vfny.geoserver.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:122)</p> FIRST - Bug #5039 (New): Errors while saving assessments on to the serverhttps://projects.ecoinformatics.org/ecoinfo/issues/50392010-06-03T15:19:52ZSandeep Namilikondasandeep.namilikonda@gmail.com
<p>Packages saved on to the server are incorrectly reported as <strong>not</strong> saved <br />in Morpho. e.g.,2007F_BS111_Exam1 (moyerbrailean.452.18)</p>
<p>Also, when a user revises an assessment package's content such as <br />modifying student data and re-uploads, the server throws a revision error<br />on the lines of "Document not found for accession number .. "</p> Kepler - Bug #5030 (New): RExpression2 actor will fail if the libs are not foundhttps://projects.ecoinformatics.org/ecoinfo/issues/50302010-05-26T21:20:31ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Creating a new bug from discussion originating in bug#4985, relevant sections posted below:</p>
<p>Jianwu said:<br />I also tried workflows in Kepler-2.0.0-Demos\demos\R\r-2.0.0\demos\JRI<br />directory, the whole Kepler just quit with the following message in the<br />console. It makes sense that the dll doesn't work for 64 bit machine. But just<br />quitting Kepler is too unfriendly.</p>
<pre><code>[null] Cannot find JRI native library!<br /> [null] Please make sure that the JRI native library is in a directory<br />liste<br />d in java.library.path.<br /> [null]<br /> [null] java.lang.UnsatisfiedLinkError: C:\Program<br />Files\Kepler-2.0-RC2\r-2.<br />0.0\lib\jri.dll: Can't load IA 32-bit .dll on a AMD 64-bit platform<br /> [null] at java.lang.ClassLoader$NativeLibrary.load(Native Method)<br /> [null] at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1753)<br /> [null] at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1678)<br /> [null] at java.lang.Runtime.loadLibrary0(Runtime.java:822)<br /> [null] at java.lang.System.loadLibrary(System.java:993)<br /> [null] at org.rosuda.JRI.Rengine.&lt;clinit&gt;(Rengine.java:19)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2._initializeRengine(REx<br />pression2.java:569)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2._fireUsingJRI(RExpress<br />ion2.java:547)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2.fire(RExpression2.java<br />:289)<br /> [null] at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br /> [null] at<br />ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSched<br />ulingDirector.java:188)<br /> [null] at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br /> [null] at ptolemy.actor.Manager.iterate(Manager.java:749)<br /> [null] at ptolemy.actor.Manager.execute(Manager.java:351)<br /> [null] at ptolemy.actor.Manager.run(Manager.java:1162)<br /> [null] at ptolemy.actor.Manager$3.run(Manager.java:1215)<br />Exception in thread "main" Java returned: 1<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br />Caused by: Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> ... 1 more<br />--- Nested Exception ---<br />Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)</code></pre>
<p>and Ben responded:<br />2. The RExpression2 (JRI-based) actor will fail if the libs are not found. This<br />is probably deep in the JRI.jar library when it cannot load the correct native<br />lib for the platform. We could probably try to detect the 32 v. 64 bitness of<br />the system and prevent the actor from attempting to use JRI if it was on a 64<br />bit machine - otherwise it will be the hard failure (system.exit)</p>
<p>and Jianwu:<br /> Matlab actors also have 32 and 64 bit issue when using JNI libraries to<br />communicate with Matlab. It will pop up an exception message when the JNI lib<br />doesn't work with the system. You can find some information at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor">https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor</a>.<br />It may help this bug.</p> FIRST - Bug #4999 (New): FIRST Website download and missing metadata issueshttps://projects.ecoinformatics.org/ecoinfo/issues/49992010-05-12T01:18:36ZSandeep Namilikondasandeep.namilikonda@gmail.com
<p>Features that used to function well seem to give inconsistent and incorrect <br />results. In an attempt to test the download feature on the FIRST website,<br />Jay synchronized an already existing package onto his laptop using Morpho,<br />made nominal edits, and saved it back on to the server so that he could <br />then try and download it from the website. Here are the issues he encountered.</p>
<p>1) When the duplicate package was uploaded to the server, the server complained<br /> about the assessment item ID (or revision number?) being smaller than <br /> the copy that was already on the server.</p>
<pre><code>So, Jay saved the package again to get around the issue.</code></pre>
<p>2) Once the package was on the server, he checked on the website to view the<br /> contents of the package. Surprisingly, he found the meta data missing from<br /> the duplicate package as well as the original package.</p>
<p>3) When he tried to download the duplicate package, he was only able to <br /> download the transposed form of it.</p>
<p>4) Later, Jay uploaded another duplicate package, this time without any<br /> metadata included. The upload made all the items from the original <br /> package not to appear on the website until Jay reopened the original<br /> package using Morpho and saved it back to the network.</p>
<p>Further attempts to download any of the packages led to ArrayOutOfBounds <br />exception.</p> Kepler - Bug #4881 (New): RExpression outputs [false] for any matrix of booleanshttps://projects.ecoinformatics.org/ecoinfo/issues/48812010-03-12T18:53:40ZOliver Soongsoong@nceas.ucsb.edu
<p>In an RExpression, add an output port "out" and use this R script:</p>
<p>out <- matrix(c(TRUE, FALSE, TRUE, FALSE), 2)</p>
<p>I get [false] as the output token, which seems to be because RExpression.java on line 1108 says:</p>
<p>mt = new BooleanMatrixToken();</p>
<p>instead of:</p>
<p>mt = new BooleanMatrixToken(valS);</p>
<p>or something similar. I'm not actually sure such a constructor exists, but it seems like it should given the other constructors in the lines before.</p> FIRST - Bug #4861 (New): NBII Connectivity Issueshttps://projects.ecoinformatics.org/ecoinfo/issues/48612010-03-02T21:55:27ZSandeep Namilikondasandeep.namilikonda@gmail.com
<p>When a user tries to associate a category from NBII vocabulary to an item,<br />an error message pops-up complaining about not being able to load the vocabulary.<br />It seems this problem could be reproduced when the user is trying to connect<br />to the server from a crowded network or at a busy time of the day.</p>
<p>It appears to be a network load issue, which could be confirmed if the <br />"timeout" or "number of retries" variable were to be extended.</p> FIRST - Bug #4406 (New): Include assessmentItemId in the Metacat indexPaths propertyhttps://projects.ecoinformatics.org/ecoinfo/issues/44062009-09-21T19:37:24Zben leinfelderleinfelder@nceas.ucsb.edu
<p>For performance - we need to remember to include:<br />"assessmentItems/assessmentItem/assessmentItemId" <br />in the metacat property:<br />"xml.indexPaths" <br />otherwise searches for assessments across items will take quite a bit more time.</p> EML - Bug #4393 (New): Use datamanager for EML QA/QChttps://projects.ecoinformatics.org/ecoinfo/issues/43932009-09-17T20:24:06Zben leinfelderleinfelder@nceas.ucsb.edu
<p>As discussed at the LTER meeting this year:<br />------------<br />Work Group: Metrics and reports for EML data package quality<br />The EML data manager library (contributors: Costa, Tao, Leinfelder, Servilla) was created to parse EML metadata documents and insert the described data entity into a relational database. Our experience using the library with data packages contributed to the LTER NIS indicates that a large fraction do not have metadata of sufficient quality for the data to be used in this way. The primary contribution from LTER sites to the NIS is data sets, which are intended to be used in cross-site synthesis projects. Clearly, for cross-site synthesis to make use of the NIS a certain minimum level of metadata and data quality is required.<br />The goals for this group:<br />1. establish a set of metrics for LTER EML data package quality,<br />2. recommend content for a report to be produced by the EML data manager library, and<br />3. consider implementation strategies, e.g. should the report be another choice on the EML parser page? a shell script similar to that included with the EML parser?</p>
<p>The quality reports can be used to<br />1. inform the dataset contributor about the content of the data package, and indicate whether data are of sufficient quality to be machine-readable. Our data catalog (metacat) has no quality standards beyond basic XML and EML compliance, so a data package that fails these quality metrics can still be uploaded or harvested, although its usefulness is limited.<br />2. in the LTER context, reports can produce a list of failure modes for LTER metadata and data entities. Such a list could provide input for the design of specific tools for data providers, or help identify gaps in a site's IM system. A site requesting supplemental funding for its IMS could use the reports as part of the proposal justification.</p>
<p>As a starting point for our discussion, I have started a flowchart based on my own experience with the data manager library and SBC's EML data packages.</p>
<p>Here is the current membership (on this cc list, and present in Estes Park):<br />Margaret O'Brien, SBC<br />Emery Boose, HFR<br />Dan Bahauddin, CDR<br />James Brunt, LNO<br />Mark Servilla, LNO<br />Duane Costa, LNO<br />Mark Shildhauer, NCEAS<br />Ben Leinfelder, NCEAS</p> FIRST - Bug #3868 (New): image does not showhttps://projects.ecoinformatics.org/ecoinfo/issues/38682009-03-08T21:04:21ZJay Leeleejon20@msu.edu
<p>When we retrieve the items from the database, it does now show image that is belonging to the item.</p> FIRST - Bug #3829 (New): Support UTF8 encoded XML in Metacathttps://projects.ecoinformatics.org/ecoinfo/issues/38292009-02-18T18:40:41Zben leinfelderleinfelder@nceas.ucsb.edu
<p>We've now added a [configurable] way to change the default text encoding when serializing XML in Morpho (using UTF8 so we can capture some of those specific cut+paste-Word-related apostrophes and hyphens that muck up plain text) but Metacat doesn't fully support serializing those XML files as the same UTF8 and returning them as such.</p> FIRST - Bug #3821 (New): Cannot launch parser within Morpho when using Java 1.6https://projects.ecoinformatics.org/ecoinfo/issues/38212009-02-17T23:54:23Zben leinfelderleinfelder@nceas.ucsb.edu
<p>We're finding this happens with Java 1.6 on both Window XP and Windows Vista.<br />The JPedal classes are not being found by the classloader from within the AWT-EventQueue thread (weird!).</p>