SEEK: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-06-09T18:14:05ZEcoinformatics Redmine
Redmine 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 #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 #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 #2422 (New): Changing Logging Options Prevent Metadata Downloadshttps://projects.ecoinformatics.org/ecoinfo/issues/24222006-04-20T18:37:01ZDavid Sledgedsledge@lternet.edu
<p>In the file log4j.properties in kepler's base directory, changing the line that reads:</p>
<pre><code>log4j.rootLogger=WARN, CONSOLE, R</code></pre>
<p>to:</p>
<pre><code>log4j.rootLogger=DEBUG, CONSOLE, R</code></pre>
<p>prevents Metadata from being downloaded from Metacat. With the ecogrid webapp--which uses the same API that kepler uses to access data on the ecogrid--the lack of a log4j.properties file prevented the metadata from being downloaded.</p>
<p>In both cases, org.ecoinformatics.ecogrid.queryservice.stub.EcoGridQueryLevelOneServiceStub.get() threw a ClassCastException.</p>
<p>Kepler:</p>
<p>java.lang.ClassCastException: java.lang.String<br /> at <br />org.ecoinformatics.ecogrid.queryservice.stub.EcoGridQueryLevelOneServiceStub.get(EcoGridQueryLevelOneServiceStub.java:310)<br /> at <br />org.ecoinformatics.ecogrid.queryservice.EcogridGetToStreamClient.get(EcogridGetToStreamClient.java:81)<br /> ...</p>
<p>Webapp:</p>
<p>java.lang.ClassCastException: java.lang.String<br /> at org.ecoinformatics.ecogrid.queryservice.stub.EcoGridQueryLevelOneServiceStub.get(Unknown Source)<br /> at org.ecoinformatics.ecogrid.queryservice.EcogridGetToStreamClient.get(Unknown Source)<br /> ...</p> Bug #1790 (New): Add ITIS data to TOS db v1.1.0https://projects.ecoinformatics.org/ecoinfo/issues/17902004-11-29T18:35:44ZAimee Stewartastewart@ku.eduBug #1648 (New): Create taxon developer web site which calculates metrics of codehttps://projects.ecoinformatics.org/ecoinfo/issues/16482004-07-27T04:11:46ZAimee Stewartastewart@ku.eduBug #1614 (New): Add concept authoring code to enterProviderDatahttps://projects.ecoinformatics.org/ecoinfo/issues/16142004-06-29T15:51:57ZAimee Stewartastewart@ku.eduBug #1403 (New): Add test database creation to build processhttps://projects.ecoinformatics.org/ecoinfo/issues/14032004-03-26T23:11:40ZAimee Stewartastewart@ku.eduBug #1402 (In Progress): Create small test database with hickory and mosseshttps://projects.ecoinformatics.org/ecoinfo/issues/14022004-03-26T23:11:18ZAimee Stewartastewart@ku.eduBug #1377 (In Progress): Create UML diagram from stubshttps://projects.ecoinformatics.org/ecoinfo/issues/13772004-03-23T21:50:26ZAimee Stewartastewart@ku.eduBug #1375 (In Progress): Add deployment target to ant build filehttps://projects.ecoinformatics.org/ecoinfo/issues/13752004-03-23T21:35:36ZAimee Stewartastewart@ku.eduBug #1336 (New): create ecology specific pipelineshttps://projects.ecoinformatics.org/ecoinfo/issues/13362004-02-09T19:07:03ZChad Berkleyberkley@nceas.ucsb.edu
<p>we need to build more ecology specific pipelines for kepler. these should be<br />the general text book type models like the lotka-volterra one that we build in<br />SEV. Rich and Mark had a long list of ones that they wanted to<br />implement...could you guys please add a list here in bugzilla?</p> Bug #1166 (In Progress): create a schema for registry metadatahttps://projects.ecoinformatics.org/ecoinfo/issues/11662003-09-26T22:09:19ZMatt Jonesjones@nceas.ucsb.edu
<p>Need a schema that defines the metadata associated with an EcoGrid Registry. <br />Minimally this is the GSH of the registry, but it also will likely include other<br />information, such as contact info for the maintainers, and mechanisms to get<br />lists of the services registered there (probably already part of the ogsa<br />registry interface). Matt agreed to start this, and Raja will review it.</p> Bug #1065 (New): create proposal for data and semantic types for workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/10652003-05-20T16:38:08ZMatt Jonesjones@nceas.ucsb.edu
<p>We need a mechanism to type input and output parameters in workflows, and to<br />type data items that are bound to workflows. These types include simple types<br />and semantic types as discussed at the May 2003 SEEK meeting. MoML has a type<br />property that is used for simple storage type declarations for ports. We need<br />to determine if we will be adding a one or more new properties to accomodate XSD<br />data types and semantic types, or if we can overload the MoML type property. It<br />is important that this typing system be compatible with WSDL.</p>
<p>To close this bug, please produce:<br />1) A proposed mechanism for binding qualified type names to ports in an<br />analytical step<br />2) A proposed serialization syntax for (1)<br />3) A modified XSD schema or other document showing the modified MoML or other<br />language for (2)</p> Bug #1059 (New): create testing harness for ecogridhttps://projects.ecoinformatics.org/ecoinfo/issues/10592003-05-19T19:57:31ZMatt Jonesjones@nceas.ucsb.edu
<p>We need a common testing harness that can be used to launch client queries<br />against ecogrid nodes and validate that the results returned are correct. This<br />system would be a basic client application, and so the core of it could be<br />reused in other clients if it is properly designed.</p>
<p>Who: Higgins<br />Target: June 9</p>