Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-05T04:56:18ZEcoinformatics Redmine
Redmine Kepler - Bug #4740 (New): Create Ontology_Catalog sql table in the CORE persistent databasehttps://projects.ecoinformatics.org/ecoinfo/issues/47402010-02-05T04:56:18ZAaron Aaronaschultz@nceas.ucsb.edu
<p>I ran into our old friend, the "Cannot Find Ontology" error. After much time trying to debug through the OntologyConfiguration and OntologyCatalog classes I discovered that the way the owl files are being accessed is very fragile and thus causes this error (which I was finally able to reproduce by ant clean-cache). The issue is how the absolute paths are being created to find the owl files. I would suggest we create a database table in the persistent core database that has four columns: ID, NAME, PATH, and LIBRARY. The PATH is the fully qualified absolute path to the OWL file on the system that Kepler is running on (so we don't have to keep trying to figure out what the absolute path is in the Java code every time we want to get to the owl file).</p>
<p>The new catalog system would work like this:<br />1.) Default owl files (that are shipped with Kepler) are defined in Java code and inserted into the table the first time Kepler is started using the fully qualified absolute path for whatever system Kepler is running on<br />2.) Tagging (or other modules) can then add ontologies to the sql table (thus not having to overwrite the ontology_catalog.xml file directly as is done now)<br />3.) The user can then edit the the catalog through a gui interface (as opposed to editing the ontology_catalog.xml file as is done now)</p> Kepler - Bug #4584 (New): CacheManager.getObject(KeplerLSID lsid) returns an object with the wron...https://projects.ecoinformatics.org/ecoinfo/issues/45842009-11-25T21:03:15ZAaron Aaronaschultz@nceas.ucsb.edu
<p>It seems that objects returned by the CacheManager.getObject(KeplerLSID lsid) method do not always have the right LSID... There is a lot of funny translation and things going on with the CacheObjects. This mechanism of storing a serialized CacheObject that contains metadata about the object in addition to the object itself is inherently fragile. I would propose that we do away with CacheObjects and use the SQL database to store metadata about objects and serialize them directly to files (instead of serializing their CacheObject counterparts). This would greatly reduce the complexity of the system.</p> Kepler - Bug #4012 (New): update documentation to explain adding actor to library via KARhttps://projects.ecoinformatics.org/ecoinfo/issues/40122009-04-22T16:29:17ZMatt Jonesjones@nceas.ucsb.edu
<p>The current Hello World Tutorial stops the tutorial at using 'Instantiate Component' to place an actor on the canvas. <br /> <a class="external" href="https://kepler-project.org/developers/teams/build/developing-a-hello-world-actor-using-the-kepler-build-system-and-eclipse">https://kepler-project.org/developers/teams/build/developing-a-hello-world-actor-using-the-kepler-build-system-and-eclipse</a><br />Most users want to also add their actor to their library pane. This is described in Sections 10.3 and 10.4 of the User Manual:<br /> <a class="external" href="https://code.kepler-project.org/code/kepler-docs/trunk/outreach/documentation/shipping/UserManual.pdf">https://code.kepler-project.org/code/kepler-docs/trunk/outreach/documentation/shipping/UserManual.pdf</a></p>
<p>The Hello World tutorial should be extended with an additional step that shows how to create a KAR file and import it into Kepler's Library. The User Manual should also be checked to be sure that the instructions are still correct.</p> SEEK - Bug #1790 (New): Add ITIS data to TOS db v1.1.0https://projects.ecoinformatics.org/ecoinfo/issues/17902004-11-29T18:35:44ZAimee Stewartastewart@ku.eduSEEK - Bug #1765 (In Progress): Investigate Hibernate for database and parser abstractionhttps://projects.ecoinformatics.org/ecoinfo/issues/17652004-11-08T15:49:18ZAimee Stewartastewart@ku.eduSEEK - Bug #1761 (In Progress): Update object model (v1.1.0) to more closely mirror TCShttps://projects.ecoinformatics.org/ecoinfo/issues/17612004-11-08T15:43:46ZAimee Stewartastewart@ku.edu
<p>Relationships are handled slightly differently, return values for<br />getRelatedConcept change, objects mirror TCS more closely.</p> SEEK - Bug #1677 (In Progress): Modify concept package objects to handle relationships for TOS v1...https://projects.ecoinformatics.org/ecoinfo/issues/16772004-09-13T17:34:46ZAimee Stewartastewart@ku.edu
<p>Create CRelationshipTo objects to be held within CConcept objects. Create<br />CRelationshipAssertion objects to be used for 3rd party relationships. Remove<br />CRelatedConcept.</p> SEEK - Bug #1673 (In Progress): Work with XSLT parser to convert ITIS data for input to Taxon DBhttps://projects.ecoinformatics.org/ecoinfo/issues/16732004-09-09T22:53:50ZAimee Stewartastewart@ku.edu
<p>Modify and use XSLT parser written by Dave Thau to convert existing ITIS data<br />from v0.51 into current (0.71) schema.</p> SEEK - 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.eduSEEK - Bug #1448 (New): Refactor ProxyFactory to create TOSProxyDispatcher or LocalCacheTOSProxyhttps://projects.ecoinformatics.org/ecoinfo/issues/14482004-04-05T19:52:16ZAimee Stewartastewart@ku.edu
<p>TOSProxyDispatcher will query multiple proxies, both distributed and local;<br />LocalCacheTOSProxy will be optimized for querying all hierarchy providers in the<br />local cache. This will be postponed to maximize the functionality by e-science,<br />and because distributed proxies will not be available immediately.</p> SEEK - Bug #1403 (New): Add test database creation to build processhttps://projects.ecoinformatics.org/ecoinfo/issues/14032004-03-26T23:11:40ZAimee Stewartastewart@ku.eduSEEK - Bug #1402 (In Progress): Create small test database with hickory and mosseshttps://projects.ecoinformatics.org/ecoinfo/issues/14022004-03-26T23:11:18ZAimee Stewartastewart@ku.eduSEEK - Bug #1397 (In Progress): Implement highest priority interfaces (first 7 of following list ...https://projects.ecoinformatics.org/ecoinfo/issues/13972004-03-26T16:48:57ZAimee Stewartastewart@ku.edu
<p>1. getConcept - takes a GUID and returns a concept<br />2. findConcept - takes a partially filled out Taxonomic Exchange Schema (TES)<br />and returns a list of concepts weighted according to the chosen similarity<br />algorithm.<br />3. compareConcept - takes 2 GUIDs and returns a measure of similarity according<br />to the chosen similarity algorithm.<br />4. enterProviderData - allows input of concepts and relationships from a<br />particular provider into the Taxon Cache.<br />5. editRelationship - add, delete or edit a relationship between concepts for a<br />particular provider.<br />6. findRelatedConcept - find parents or children at a certain distance from a<br />given concept (grandparents, grandchildren, etc) according to a particular provider.<br />7. measureRelationship - takes 2 GUIDs and returns a measure of the relationship<br />according to the chosen relate algorithm.<br />8. compareConceptRelationships - takes a 2 concepts and 2 providers and compares<br />their positions within their respective trees according to the chosen relate<br />algorithm.<br />9. compareConceptLists - more discussion is needed on the requirements for this<br />method. Previously implemented methods should form the basis for the<br />implementation.</p> SEEK - Bug #1377 (In Progress): Create UML diagram from stubshttps://projects.ecoinformatics.org/ecoinfo/issues/13772004-03-23T21:50:26ZAimee Stewartastewart@ku.eduSEEK - Bug #1375 (In Progress): Add deployment target to ant build filehttps://projects.ecoinformatics.org/ecoinfo/issues/13752004-03-23T21:35:36ZAimee Stewartastewart@ku.edu