SEEK: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362006-12-09T00:20:15ZEcoinformatics Redmine
Redmine 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 #2301 (New): deploy ecogrid-1.0.0beta2 services for metacat, srb, digir, geonhttps://projects.ecoinformatics.org/ecoinfo/issues/23012005-11-29T21:28:11ZMatt Jonesjones@nceas.ucsb.edu
<p>Need to coordinate the deployment of the beta2 release so that all services are<br />deployed at the same time. Deployment really can not occur until all of the<br />migration to web services bugs are complete (bug 2294, bug 2295, bug 2296, bug<br />2297, bug 2298).</p> Bug #2291 (New): define faults for all EcoGrid serviceshttps://projects.ecoinformatics.org/ecoinfo/issues/22912005-11-29T20:12:02ZMatt Jonesjones@nceas.ucsb.edu
<p>The current API needs to be modified to be able to pass back faults for error<br />conditions. To close this bug, we need to:</p>
<p>1) design an intelligent set of faults that covers conceivable error conditions<br />and provides a human readable message appropriate for display to users<br />2) add these faults to the WSDL definitions of the ecogrid apis, making sure to<br />support both SOAP and HTTP bindings where they exist<br />3) implement the faults for each of the services (metacat, digir, srb)</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 #1663 (New): Create web prototypehttps://projects.ecoinformatics.org/ecoinfo/issues/16632004-08-30T21:34:39ZRobert Galesrgales@eecs.ku.edu
<p>By TDWG - Create a web-based prototype of the current version of the Taxon<br />service that is easily modified for future versions</p> Bug #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 #1596 (New): data integration of Niche Modeling in Ecogridhttps://projects.ecoinformatics.org/ecoinfo/issues/15962004-06-08T17:56:51ZBing Zhubzhu@sdsc.edu
<p>The goal of the task is to use existing data model within Ecogrid system such <br />as SRB to upload (bulkload) image files of Niche Modeling led by David <br />Stockwell into an Ecogrid data source, initially targeting at SRB system. <br />Metadata for image files is also injested into a backend database for the <br />chosen data management system such as MCAT in SRB.</p>
<p>With data stored in a Ecogrid data source, David can build Kepler workflow <br />using our Ecogrid calls to query and retrieve data from Ecogrid in the future.</p>
<p>Currently uploading data into SRB uses native SRB commands. This approach will <br />be replaced by Ecogrid's PUT call after it is implemented.</p> Bug #1403 (New): Add test database creation to build processhttps://projects.ecoinformatics.org/ecoinfo/issues/14032004-03-26T23:11:40ZAimee 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 #1158 (New): create wsdl for ecogrid query level III interfaceshttps://projects.ecoinformatics.org/ecoinfo/issues/11582003-09-26T21:08:47ZMatt Jonesjones@nceas.ucsb.edu
<p>During Seattle, we redefined the WSDL interfaces for the query operations for<br />the level III operations. <br />They now should contain:</p>
<p>Level III<br />---------<br /> FileHandle open(EcoGridIdentifier, ProxyCertificate)<br /> MimeContent read(FileHandle, Length, ProxyCertificate)<br /> void seek(FileHandle, Offset)<br /> void close(FileHandle, ProxyCertificate)</p>
<pre><code>MimeContent logicalQuery(EcoGridIdentifier, DataQueryType)<br /> -- this operation probably needs to be renamed</code></pre>
<p>For all of these methods, if "ProxyCertificate" is null, then the method should<br />be executed anonomously with only the rights of an anonymous user.</p>
<p>Peter agreed to tackle these revisions, and we agreed that these are only<br />initial thoughts on these more advanced interfaces, and that they would need to<br />be revised as we gain more experience later.</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>