SEEK: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362004-05-25T13:58:01ZEcoinformatics Redmine
Redmine Bug #1578 (Resolved): Modify Ant build so Tomcat is functional on both Linux and Windowshttps://projects.ecoinformatics.org/ecoinfo/issues/15782004-05-25T13:58:01ZAimee Stewartastewart@ku.eduBug #1577 (In Progress): Implement AddRelationshiphttps://projects.ecoinformatics.org/ecoinfo/issues/15772004-05-25T13:56:18ZAimee Stewartastewart@ku.eduBug #1576 (In Progress): Implement EnterProviderData for TOS v1.1.0 with input TCShttps://projects.ecoinformatics.org/ecoinfo/issues/15762004-05-25T13:55:13ZAimee Stewartastewart@ku.eduBug #1575 (Resolved): Modify or add objects to match new Taxonomic Exchange Schemahttps://projects.ecoinformatics.org/ecoinfo/issues/15752004-05-25T13:53:37ZAimee Stewartastewart@ku.eduBug #1527 (Resolved): Complete the documentation for WSDL and email SEEK-sms-kr & Shawnhttps://projects.ecoinformatics.org/ecoinfo/issues/15272004-04-21T21:11:45ZAimee Stewartastewart@ku.eduBug #1205 (Resolved): Get DiGIR working on Windowshttps://projects.ecoinformatics.org/ecoinfo/issues/12052003-11-06T13:15:49ZRod Spearsrods@ku.edu
<p>Need to get DiGIR working on my Windows box so I can start developing the Java<br />Wrapper</p> Bug #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 #1069 (Resolved): contact Ptolemy project about collaborationhttps://projects.ecoinformatics.org/ecoinfo/issues/10692003-05-20T17:03:49ZMatt Jonesjones@nceas.ucsb.edu
<p>Ptolemy has a lot of potential for collaboration. Need to contact the Ptolemy<br />folks to determine where oppoortunities might be, and how we might be able to<br />contribute to the project (e.g., if we develop semantic extensions, how can we<br />contribute them).</p>
<p>Possible means of contact include:<br />1) Rich visits them at Berkley<br />2) We have a teleconference to follow up<br />3) We invite one or more of them to our annual meeting in October</p> Bug #1068 (Resolved): create and analyze example pipelines with workflow editorhttps://projects.ecoinformatics.org/ecoinfo/issues/10682003-05-20T17:00:54ZMatt Jonesjones@nceas.ucsb.edu
<p>Need to create several representative formal workflows using the workflow editor<br />described in bug 1064 to show what typical workflow scenarios are. One or two<br />of these should be focused around the GARP case study. Several others should be<br />from other areas of ecology to get some breadth.</p>
<p>Once these have been created, need to:<br /> 1) review workflows to see if scientists agree that the representation is correct<br /> 2) analyze the workflows to see if there are constructs that were difficult or<br />impossible (indicating the need for a more expressive system)<br /> 3) analyze the workflows for use in developing semantic type ontologies</p> Bug #1067 (Resolved): follow up with GeoVista Studiohttps://projects.ecoinformatics.org/ecoinfo/issues/10672003-05-20T16:54:57ZMatt Jonesjones@nceas.ucsb.edu
<p>Need to explore the use of GeoVista Studio for use in SEEK. Create a GARP<br />visualization and see how easy it is to use, and how it might be modified to<br />suit our purposes. Issues to explore:</p>
<p>How hard is it to create a visualization from scratch?<br />Is the execution model well-established, and can it be changed as it can in Ptolemy?<br />Can an executing application like the ptolemy engine link its output to GV<br />Studio for visualization and further analysis?<br />How hard would it be to serialize the GV Studio workflow into an open workflow<br />language like MoML or DPML?<br />How does GV Studio link concepts (semantic type) to data?</p>
<p>Please summarize the findings here.</p> Bug #1066 (Resolved): follow up with DiscoveryNethttps://projects.ecoinformatics.org/ecoinfo/issues/10662003-05-20T16:48:29ZMatt Jonesjones@nceas.ucsb.edu
<p>Collaboration opportunities with DiscoveryNet are promising, but we need to<br />follow up withthem to determine if and how such a collaboraiton would work. <br />Issues to consider:</p>
<p>What are our current requirements for direct collaboration?<br /> -- is source code required? open source required?<br /> -- is a pricing model needed to reach environmental scientists?<br />Can DiscoveryNet be run as a backend engine without visualization?<br />Can the workflow editor be run without the execution engine?<br />Can DPML be extended to support semantic types?<br />What is the SDK API for DiscoveryNet? Can we get a copy for use in SEEK?<br />Can we get an evaluation version for use in SEEK?</p>
<p>Need to establish conference call with Yike Guo to work out these issues.</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 #1063 (Resolved): review and summarize workflow languageshttps://projects.ecoinformatics.org/ecoinfo/issues/10632003-05-20T16:21:42ZMatt Jonesjones@nceas.ucsb.edu
<p>Need a review of the features and issues associated with the various workflow<br />languages under consideration. This should turn into a recommendation of one of<br />the languages for use in SEEK. The current languages that should be examined<br />include:<br /> MoML, DPML, PMML, VDL/Chimera, XPDL, and Monarch's Pipeline language</p>
<p>Some issues to consider in the review:<br /> 1) flexibility for representing workflows (e.g., cycles)<br /> 2) support for data typing, extension to semantic typing<br /> 3) support for multiple execution models<br /> 4) static representation in open (e.g., text) format</p>
<p>Please summarize findings here.</p> Bug #1057 (Resolved): Adapt and adopt general purpose XQuery tokenizerhttps://projects.ecoinformatics.org/ecoinfo/issues/10572003-05-16T17:08:07ZMatt Jonesjones@nceas.ucsb.edu
<p>We need a general purpose XQuery tokenizer that can be used by the various<br />back-end wrapper implementations to factor out common query processing needs. <br />Best if this was available inmultiple languages or is somehow cross-platform.</p>
<p>Who: Bing, Jing<br />Target date: May 26</p> Bug #1056 (Resolved): XQuery research: processors, SQL translators, XQuery exampleshttps://projects.ecoinformatics.org/ecoinfo/issues/10562003-05-16T17:03:26ZMatt Jonesjones@nceas.ucsb.edu
<p>Research the pros and cons of using XQuery as a standard language for query<br />specs in EcoGrid.</p>
<p>Who: Peter, Bing, Jing<br />Target date: May 26</p>