SEEK: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362004-07-27T04:11:46ZEcoinformatics Redmine
Redmine 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 #1618 (In Progress): Fix rank representation in dbhttps://projects.ecoinformatics.org/ecoinfo/issues/16182004-07-06T16:12:39ZRobert Galesrgales@eecs.ku.edu
<p>The current representation of rank does not fully support the Napier schema for<br />adding a concept to the Taxon cache.</p> Bug #1615 (New): Look at KNB LDAP interface for user-friendly concept authoring authenticationhttps://projects.ecoinformatics.org/ecoinfo/issues/16152004-06-29T15:53:47ZAimee Stewartastewart@ku.eduBug #1603 (In Progress): Implement addConcepthttps://projects.ecoinformatics.org/ecoinfo/issues/16032004-06-14T19:46:21ZRobert Galesrgales@eecs.ku.edu
<p>Add implementation of addConcept as a public SOAP accessible method</p> Bug #1599 (New): integration of LSID system and taxon serverhttps://projects.ecoinformatics.org/ecoinfo/issues/15992004-06-08T18:35:32Zdave thauthau@learningsite.com
<p>Provide an LSID front end to the taxon server. This initially involves <br />supporting the traditional LSID calls getData() getMetaData(). Secondarily, <br />it involves providing access to the taxon server API through the LSID server.</p> Bug #1598 (New): integration of user management tools with taxonomic informationhttps://projects.ecoinformatics.org/ecoinfo/issues/15982004-06-08T18:32:44Zdave thauthau@learningsite.com
<p>Users (and administrators) will want to track which LSIDs have been issued and <br />which concepts have been registered.</p>
<p>This task provides tools for users to list the taxonomic concepts they've <br />entered, and make allowable edits to those concepts.</p>
<p>LSIDs are assigned by a person. That person may want to retire and reassign <br />their LSIDs someone else. This facility falls under this task as well.</p> Bug #1597 (New): initial user management system for taxon serverhttps://projects.ecoinformatics.org/ecoinfo/issues/15972004-06-08T18:27:45Zdave thauthau@learningsite.com
<p>Because many people will be contributing information to the taxonomic concept <br />server, we need to manage information about users, and allow those users to <br />manage their own information. The taxonomic server should be extended to <br />provide these capabilities.</p>
<p>This task is the creation of integrating intial user management code into the <br />taxon server:</p>
<p>join/login/logout<br />add information / edit information</p>
<p>administration tools<br /> freeze account<br /> change password<br /> email users</p> Bug #1577 (In Progress): Implement AddRelationshiphttps://projects.ecoinformatics.org/ecoinfo/issues/15772004-05-25T13:56:18ZAimee Stewartastewart@ku.eduBug #1450 (In Progress): Implement two different relate algorithmshttps://projects.ecoinformatics.org/ecoinfo/issues/14502004-04-05T20:54:42ZRobert Galesrgales@eecs.ku.edu
<p>Implement two different algorithms for calculating the similarity of two <br />taxonomy trees (subtrees), i.e., algorithms that implement the <br />IRelateAlgorithm interface.</p> 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> Bug #1403 (New): Add test database creation to build processhttps://projects.ecoinformatics.org/ecoinfo/issues/14032004-03-26T23:11:40ZAimee Stewartastewart@ku.eduBug #1397 (In Progress): Implement highest priority interfaces (first 7 of following list of 9)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> Bug #1377 (In Progress): Create UML diagram from stubshttps://projects.ecoinformatics.org/ecoinfo/issues/13772004-03-23T21:50:26ZAimee Stewartastewart@ku.eduBug #1070 (New): propose a flexible system for transformation stepshttps://projects.ecoinformatics.org/ecoinfo/issues/10702003-05-20T17:16:49ZMatt Jonesjones@nceas.ucsb.edu
<p>In any workflow, linking any two steps is likely to require some sort of<br />transformation to get the outputs of one step to match the inputs of the next. <br />This transformation is sometimes a simple cast (e.g., int -> float), sometimes a<br />more complex cast (e.g., string -> date), sometimes will require more complex<br />processing (e.g., statistical processing), and sometimes will require schema<br />transformations. In all cases, the transformation between step A and step Z can<br />be represented as one or more intermediate tansformation steps:<br /> A -> T1 -> T2 -> TN -> Z</p>
<p>Our challenge includes:</p>
<p>1) use the SMS to locate candidate transformation steps T1..TN based on type<br />signature and ontologies<br />2) determine how to generate transformation steps automatically for simple<br />transforms such as unit conversions<br />3) create a simple GUI for creating transformation steps that map between two<br />existing steps<br />4) determine the pros and cons of having transformation steps be directly<br />associated with links (e.g., a link property) rather than simply introducing new<br />transform steps that do the same tasks directly into the pipeline</p>
<p>So, the objective of this bug is to:<br />1) propose a flexible system for discovering and generating transformation steps<br />2) identify the suite of complex issues involved in generating a mapping from<br />one step to another (especially when this might require several intermediate steps)<br />3) propose a plan of work for completing this plan</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>