SEEK: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-06-09T18:32:12ZEcoinformatics Redmine
Redmine Bug #3387 (New): ontology validationhttps://projects.ecoinformatics.org/ecoinfo/issues/33872008-06-09T18:32:12ZChad Berkleyberkley@nceas.ucsb.edu
<p>when an ontology is uploaded to metacat it should be validated in several ways (in addition to the xml validation that metacat already does):</p>
<ul>
<li>if it references other documents, the user should be asked to upload those documents as well.</li>
<li>referential integrity should be checked</li>
<li>owl validitiy should be checked</li>
</ul>
<p>Any errors should be reported back to the user.</p> Bug #3386 (New): ontology management with metacathttps://projects.ecoinformatics.org/ecoinfo/issues/33862008-06-09T18:17:33ZChad Berkleyberkley@nceas.ucsb.edu
<p>User should be able to browse ontologies in the system. Should also be able to update existing ontologies.</p> Bug #3385 (In Progress): create ontology upload interfacehttps://projects.ecoinformatics.org/ecoinfo/issues/33852008-06-09T18:14:05ZChad Berkleyberkley@nceas.ucsb.edu
<p>The interface should accept an onotology, upload it to metacat and respond with the URL of the uploaded ontology. The uploaded ontology will need to have the xmlns, xml:base and xml:<namespace> attributes updated with the new url.</p>
<p>example ontology:<br /><a class="external" href="http://code.ecoinformatics.org/code/semtools/trunk/dev/oboe/oboe.owl">http://code.ecoinformatics.org/code/semtools/trunk/dev/oboe/oboe.owl</a></p> Bug #3145 (New): Fix [or remove] web interface for ecogrid queryhttps://projects.ecoinformatics.org/ecoinfo/issues/31452008-02-11T22:05:25Zben leinfelderleinfelder@nceas.ucsb.edu
<p>The Kepler user manual docs (chapter 6) have link to:<br /><a class="external" href="http://seek.ecoinformatics.org/Wiki.jsp?page=EarthGridPortal">http://seek.ecoinformatics.org/Wiki.jsp?page=EarthGridPortal</a><br />which in turn has a link to:<br /><a class="external" href="http://ecogrid.ecoinformatics.org/ecogrid/advancedQuery.jspx">http://ecogrid.ecoinformatics.org/ecogrid/advancedQuery.jspx</a></p>
<p>This search returns no data for KNB. Jing and I suspect it is due to the change in ecogrid query service names. The search should probably be updated to reflect those new endpoints. Also note that it has an option for searching GEON, too. The GEON service has not been operational for sometime, and could also be commented out, at the very least.</p> Bug #3112 (New): Deploy ecogrid-1.0.0 services for DiGIR and enforce namespaceshttps://projects.ecoinformatics.org/ecoinfo/issues/31122008-01-30T18:52:54Zben leinfelderleinfelder@nceas.ucsb.edu
<p>It was originally thought that the change in ecogrid namespaces (beta to 1.0) would be incompatible with the current DigirQueryService deployment (using beta namespaces). This appears not to be the case (they work together!) But, really, the namespaces <em>should</em> be enforced.<br />When the enhancements for doing faster (cached?) and better (dynamic providers listing?) digir queries are ready, we should deploy an updated version of this service.<br />Dave Vieglais sounds keen on this and will assist.</p> Bug #2731 (New): Make TCS document the direct data sourcehttps://projects.ecoinformatics.org/ecoinfo/issues/27312007-01-17T01:35:00Zxianhua liurobertliu325@yahoo.com
<p>Develop new functions to directly access TCS document.</p> Bug #2730 (New): Publication problemhttps://projects.ecoinformatics.org/ecoinfo/issues/27302007-01-17T01:30:39Zxianhua liurobertliu325@yahoo.com
<p>For publication let's use be use to implement both short and long full text and guid. The rest is unnecessary for now.</p> Bug #2729 (New): Support third party parent-child relationshiphttps://projects.ecoinformatics.org/ecoinfo/issues/27292007-01-17T01:28:45Zxianhua liurobertliu325@yahoo.com
<p>Third party parent-child, and should we allow parents to be specified for genus in definition.</p> Bug #2728 (New): XML Output problemhttps://projects.ecoinformatics.org/ecoinfo/issues/27282007-01-17T01:23:45Zxianhua liurobertliu325@yahoo.com
<p>Mostly validation was fine, but one minor problem was <br />identified. TaxonRankEnum X puts in string like genus, when <br />should be TaxonomicRankGenusEnum. Suggest validate with XMLSpy or <br />Oxygen</p> Bug #2727 (New): lost data during importhttps://projects.ecoinformatics.org/ecoinfo/issues/27272007-01-17T01:20:04Zxianhua liurobertliu325@yahoo.com
<p>One problem is that superfluous stuff is lost. For example:<br /><teeth>Y-5 molar pattern</teeth><br />We should capture all this in some form of buffer so it can be <br />exported. For example, all 18 relationship types shoudl come in and go out.</p> Bug #2694 (New): Change get operation in EcoGridQueryInterfaceLevelOne from soap binding to http ...https://projects.ecoinformatics.org/ecoinfo/issues/26942006-12-09T00:20:15ZJing Taotao@nceas.ucsb.edu
<p>Since ecogrid now is using pure axis web service, it is time to change get operation from soap binding to http binding. Http binding will use streaming and wouldn't use huge memory for getting big data set.</p> Bug #2693 (New): Ecogrid doesn't support relative URI in namespace element of query.xsdhttps://projects.ecoinformatics.org/ecoinfo/issues/26932006-12-09T00:13:40ZJing Taotao@nceas.ucsb.edu
<p>In query.xsd there is a elemen named namespace and its type is anyURI. In auto-generated stub, the element was assigned a java object - org.apache.axis.types.URI and used consctutor is <abbr title="String url">URI</abbr>. This consctor doesn't support relative URI.</p> Bug #2682 (New): Add start and stop dates to concepts and relationshipshttps://projects.ecoinformatics.org/ecoinfo/issues/26822006-11-27T17:10:40ZRobert Peetpeet@unc.edu
<p>We need to add start (and probably stop) dates to concepts and relationships for use with references that are continuously changing. We track Alan Weakley's concepts and relationships in conceptmapper, but Alan is continuously making changes and we need to be able to reconstruct his perspective at any given time, beause otherwise the work is not citable. The alternative solution is to have an enormous number of Weakley references, perhaps thousands in any given year. We could use just start dates and do some logical sorting to find the most recent relevant concept or relationship, but the inclusion of end dates (a minor denormalization?) would make the situation clearer and computationally more tractable. I am not at all sure how to embed start and stop dates in TCS. Perhaps we need our own upgrade to TCS. I will copy this to Jessie and Aimee to see if they have advice.</p> Bug #2650 (New): ecogrid returnfields need to support more xpathhttps://projects.ecoinformatics.org/ecoinfo/issues/26502006-11-08T18:26:25ZChad Berkleyberkley@nceas.ucsb.edu
<p>When you are dealing with documents that store a lot of information in xml attributes instead of CDATA nodes, it is imperative that xpath attribute queries work correctly. AFAICT, they don't work at all with the ecogrid returnfields. For instance, the element:</p>
<p><property name="semanticType000" class="org.kepler.sms.SemanticType" <br /> value="urn:lsid:localhost:onto:1:1#Variable"><br /></property></p>
<p>The only meaniful way to get one of the attributes values based on another is via an attribute query like:</p>
<p>//property/[@name='semanticType000']/@value</p>
<p>which should return the value attribute of any property node with a name attribute equal to 'semanticType000'.</p> Bug #2649 (New): Ecogrid returnfields don't return enough informationhttps://projects.ecoinformatics.org/ecoinfo/issues/26492006-11-08T18:21:16ZChad Berkleyberkley@nceas.ucsb.edu
<p>When using returnfields in an ecogrid query, the original xpath used in the returnfield is not returned with the results, making it very difficult to parse the results. When a query is submited, a ResultsetTypeRecordReturnfield object is returned. This object only has two useful methods: get_value() and getId(). I thought getId() would return the original xpath query used to create the returnfield, but instead it returns a cryptic identifier starting with 'f' then a number.</p>
<p>Example:<br />Given these returnfields:<br /><returnField>/entity/@name</returnField><br /><returnField>/entity/property/@name</returnField><br /><returnField>/entity/property/@value</returnField></p>
<p>And this input document:</p>
<p><entity name="Variable Setter" class="ptolemy.kernel.ComponentEntity"><br /> <property name="entityId" value="urn:lsid:kepler-project.org:actor:10:2" <br /> class="org.kepler.moml.NamedObjId"/><br /> <property name="documentation" class="org.kepler.moml.DocumentationAttribute"><br /> null<br /> </property></p>
<pre><code>&lt;property name="class" value="ptolemy.actor.lib.SetVariable" <br /> class="ptolemy.kernel.util.StringAttribute"><br /> &lt;property name="id" value="null" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;/property&gt;</code></pre>
<pre><code>&lt;property name="kepler:input" class="org.kepler.moml.PortAttribute"&gt;<br /> &lt;property name="direction" value="input" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;property name="dataType" value="unknown" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;property name="isMultiport" value="false" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;/property&gt;</code></pre>
<pre><code>&lt;property name="variableName" class="ptolemy.kernel.util.StringAttribute" <br /> value="parameter"><br /> &lt;/property&gt;<br /> &lt;property name="delayed" class="ptolemy.data.expr.Parameter" value="true"&gt;<br /> &lt;/property&gt;<br /> &lt;property name="semanticType000" class="org.kepler.sms.SemanticType" <br /> value="urn:lsid:localhost:onto:1:1#Variable"><br /> &lt;/property&gt;<br /> &lt;property name="semanticType111" class="org.kepler.sms.SemanticType" <br /> value="urn:lsid:localhost:onto:2:1#LocalInput"><br /> &lt;/property&gt;<br /> &lt;property name="_location" class="ptolemy.kernel.util.Location" <br /> value="{250, 300}"><br /> &lt;/property&gt;<br /> &lt;property name="karId" class="ptolemy.kernel.util.StringAttribute" <br /> value="urn:lsid:kepler-project.org:kar:11:1"><br /> &lt;/property&gt;<br />&lt;/entity&gt;</code></pre>
<p>You will get returnfields (in the format getId():get_value()) like this:<br />returnfield: f0:Variable Setter<br />returnfield: f1:entityId<br />returnfield: f2:urn:lsid:kepler-project.org:actor:10:2<br />returnfield: f1:documentation<br />returnfield: f1:class<br />returnfield: f2:ptolemy.actor.lib.SetVariable<br />returnfield: f1:kepler:input<br />returnfield: f1:variableName<br />returnfield: f2:parameter<br />returnfield: f1:delayed<br />returnfield: f2:true<br />returnfield: f1:semanticType000<br />returnfield: f2:urn:lsid:localhost:onto:1:1#Variable<br />returnfield: f1:semanticType111<br />returnfield: f2:urn:lsid:localhost:onto:2:1#LocalInput<br />returnfield: f1:_location<br />returnfield: f2:{250, 300}<br />returnfield: f1:karId<br />returnfield: f2:urn:lsid:kepler-project.org:kar:11:1</p>
<p>Instead, there either needs to be a new method, getQuery(), that would return the query for each field, or the getId() should return the query or some other more meaninful identifier.</p>