From rich at sfsu.edu Sun Aug 1 18:52:13 2004 From: rich at sfsu.edu (Rich Williams) Date: Sun, 1 Aug 2004 18:52:13 -0700 Subject: [seek-reports] (no subject) In-Reply-To: Message-ID: 1) Completed tasks/bugs fixed None 2) Current Work and Bugs Worked with Serguei on getting GrOWL ready for an alpha release. Worked on building OWL model from graph structure, the metadata panel user interface and made extensive modifications to the OWL rendering in OWLAPI, fixing bugs and adding unimplemented features. 3) Significant issues None From Serguei.Krivov at uvm.edu Mon Aug 2 08:00:49 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Mon, 2 Aug 2004 11:00:49 -0400 Subject: [seek-reports] progress report growl Message-ID: <000001c478a1$7f2efc70$3ca6c684@BTS2K3000D5635086B> Progress Report 08- 02-2004 Serguei Krivov 1) Completed tasks/bugs fixed -Changed code for search boxes -Changed rendering of enumerations and data enumerations making them consistent with other set operators -Extensive testing and minor bug fixes 2) Current Work and Bugs -growl applet for IMA. This will be stripped version of the current editor -smart selection of property restriction names (controversial) 3) Significant issues Should we allow user to specify property restrictions without first specifying the property? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040802/cc092040/attachment.htm From xianhual at email.unc.edu Mon Aug 2 08:00:48 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 02 Aug 2004 11:00:48 -0400 Subject: [seek-reports] report Message-ID: <1091458848.410e572088c27@webmail7.isis.unc.edu> Status report Xianhua Liu August 2, 2004 Completed Tasks/ Bugs Fixed: -------------------------------------------------------------------- Current Work and Bugs: ------------------------------------------------------------------- * Design Taxonomic Concept Browser & Editor(TCBE) Significant Issues ------------------------------------------------------------------- * How could TCBE be applied to different Taxonomic Models, like SEEK Data Model and VegBank? 1. Introducing high abstraction of 'Model' 2. a 'Model' will be defined through specifying its components, such as 'NAME','REFERENCE','TAXON CONCEPT', 'INTER-CONCEPT RELATIONSHIP' and 'STATUS' and so on. 3. Users need to define their specific 'Models' and how data can be retrieved from database and put into their 'Models' before they can use TCBE to access the data. ------------------------------------------------------------------- From rgales at eecs.ku.edu Mon Aug 2 15:11:57 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 02 Aug 2004 17:11:57 -0500 Subject: [seek-reports] Status Report 7-26 to 7-31 2004 Message-ID: <410EBC2D.7070503@eecs.ku.edu> Status Report Robert Gales Aug 2, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Completed the first draft of a proposal schema containing modifications to allow for reuse of lower level taxonomic information, restructuring for more efficient parsing, and creation and authoring of relationships between concepts and/or lower level taxonomic data without the need to create new concepts. * Participated in two teleconference calls regarding the proposed changes to the schema Current Work and Bugs: ---------------------- * Comparing the strengths and weaknesses of both schemas and determining any implementation assumptions the two schemas make Significant Issues ------------------ * Nothing new From jwang at sdsc.edu Mon Aug 2 15:15:48 2004 From: jwang at sdsc.edu (Jenny Wang) Date: Mon, 2 Aug 2004 15:15:48 -0700 (PDT) Subject: [seek-reports] Weekly report Message-ID: Weekly report "Jenny" Guilian Wang August 1, 2004 Completed Tasks/Bugs Fixed: ---------------------------- * Tested the feasibility of wrapping the schema tool as an actor in Kepler. It works as a stand-alone actor, but runs super slow. Further efforts are needed to make it useful for data transformation between actors in pipelines. * Fix a bug in the gui of the tool: consistently highlight where user attention is needed. Current Work and Bugs: ---------------------- * Continue to connect Kepler with our schema matching tool by wrapping it as an actor able to perform data transformation between its previous actor and the next actor. * Work on 2 paper drafts * Fix more bugs of the tool: 1) polish the arrow panel for indicating where it is working on in the GUI: adjustable as GUI changes, etc. 2) correctly handle union types of matches identified during matching process. * Implement abstract schemas and abstract schema morphisms to make the tool more general: focus on designing a schema morphism interface and implementing it. Significant Issues: ------------------- From bzhu at sdsc.edu Mon Aug 2 18:39:43 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 2 Aug 2004 18:39:43 -0700 Subject: [seek-reports] status report from Bing Zhu - Aug 2 Message-ID: Completed Tasks/Bugs Fixed: - revision of the 'put' gwsdl for ecogrid. (The file is checked into SEEK CVS place.) - demo of whywhere data at UCSD SEEK meeting. - had 2 meetings with Efrat for the initial design of SRB actors Current Work and Bugs: - implementation of pgm_cut in ecogrid's node in Orion. - implementation of ecogrid's put function Significant Issues: - none From higgins at nceas.ucsb.edu Tue Aug 3 06:10:07 2004 From: higgins at nceas.ucsb.edu (Dan Higgins) Date: Tue, 03 Aug 2004 06:10:07 -0700 Subject: [seek-reports] Status Report - Aug 2,2004 - Dan Higgins Message-ID: <410F8EAF.5060106@nceas.ucsb.edu> Status report Dan Higgins Aug 2, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Completed samples of an alternative EML Data Source (EML200DataSource2) which does not create ports for each of the columns in a table. Instead, it contains ports which provide the datatable as a string along with metadata needed to process the table data (e.g. delimiter, number of columns). Several sample workflows using this actor were created and checked in to the kepler module. These include 'eml-simple-datadisplay.xml' and 'eml-simple-plot.xml' in the 'eco' directory and 'eml-simple-RPlot.xml' in the 'R' directory. The later shows how ecogrid eml data can be feed into an instance of 'R' for analysis and plotting. Current Work and Bugs: ---------------------- * Worked on understanding the full Garp workflow and what needs to be done to finish various incomplete pieces of that workflow. * Examing the 'Generic Mapping Tools' system for code that can be used in Kepler. This toolkit (http://gmt.soest.hawaii.edu/) has numerous mapping tools in the form of standalone commandline executables that may be of use as Kepler actors. * Examing how to create a Java interface to R that is more direct than using a subprocess and text/strings. Possibilities include: 1) http://www.omegahat.org/RSJava/ and 2) http://stats.math.uni-augsburg.de/JGR/ [ The JGR (2) is interesting because it provides a Java based grapics display for 'R' which we may be able to integrate into Kepler!] Significant Issues ------------------ * None From rods at ku.edu Tue Aug 3 08:06:15 2004 From: rods at ku.edu (Rod Spears) Date: Tue, 03 Aug 2004 10:06:15 -0500 Subject: [seek-reports] Status 7/26 - 7/30 Message-ID: <410FA9E7.6010401@ku.edu> Completed Tasks/ Bugs Fixed: * Completed the XML serializer and desserializer for the schema objects and for the query objects * Fixed some UI bugs * Added additional panes for adding tables to the join builder Current Work and Bugs: * Continued on Bug 1595 - Create Advance Query Builder UI Important or Outstanding Issues (of a significant nature) * None Work This Week: * Finish initial phase of work on Bug 1595 - Create Advance Query Builder UI -- Rod Spears Biodiversity Research Center University of Kansas 1345 Jayhawk Boulevard Lawrence, KS 66045, USA Tel: 785 864-4082, Fax: 785 864-5335 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040803/687e4b4b/attachment.htm From tao at nceas.ucsb.edu Tue Aug 3 09:13:23 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Tue, 3 Aug 2004 09:13:23 -0700 (PDT) Subject: [seek-reports] Status report In-Reply-To: Message-ID: Status Report Jing Tao 08/03/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Installation of metacat ecogrid production node in NCEAS Current Work and Bugs: ---------------------- * Query engine against data object in Kepler Significant Issues ------------------ * None -- Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From xianhual at email.unc.edu Mon Aug 9 06:45:00 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 09 Aug 2004 09:45:00 -0400 Subject: [seek-reports] seek-report this week: xianhua Message-ID: <1092059100.41177fdc27167@webmail1.isis.unc.edu> Status report Xianhua Liu August 9, 2004 Completed Tasks/ Bugs Fixed: -------------------------------------------------------------------- * Revised the Design of Taxonomic Concept Browser & Editor(TCBE) * Wrote comments and attended the group conference call about Transfer Schema Current Work and Bugs: ------------------------------------------------------------------- * Designing Taxonomic Concept Browser & Editor(TCBE) * Studying OWL and GROWL and their applications in TCBE Significant Issues ------------------------------------------------------------------- * ------------------------------------------------------------------- From higgins at nceas.ucsb.edu Mon Aug 9 09:10:25 2004 From: higgins at nceas.ucsb.edu (Dan Higgins) Date: Mon, 09 Aug 2004 09:10:25 -0700 Subject: [seek-reports] Status Report - Dan Higgins - 8/9/2004 Message-ID: <4117A1F1.1020201@nceas.ucsb.edu> 1) Completed tasks/bugs fixed -- Virtually the entire week was spent in helping Chad implement scrollbars within the Kepler graph pane. The problem was understanding just how the AffineTransformations and Java 2D system was being used in Ptolemy panner and display. The scrollbar system is now working (in a branch of CVS) and integrated with the panner! 2) Current Work and Bugs -- Contuing work on integrating 'R' and other processes into Kepler 3) Significant issues -- none -- ******************************************************************* Dan Higgins higgins at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Ph: 805-892-2531 National Center for Ecological Analysis and Synthesis (NCEAS) 735 State Street - Room 205 Santa Barbara, CA 93195 ******************************************************************* From berkley at nceas.ucsb.edu Mon Aug 9 11:40:12 2004 From: berkley at nceas.ucsb.edu (Chad Berkley) Date: Mon, 9 Aug 2004 11:40:12 -0700 Subject: [seek-reports] 8/2-8/6 Message-ID: <8C8BB0BA-EA33-11D8-BD83-000A95DA7EF8@nceas.ucsb.edu> 1) Completed tasks/bugs fixed --added a search panel to the actor library in kepler 2) Current Work and Bugs --still need to refine the resultset of the actor library search --need to get the tree to reconfigure itself with just the search results --need to fix the actory library tab pane so that it resizes correctly --integrate dan's fixed scrollbar code into the code base and get it to work with the configuration options so you can turn scrollbars off 3) Significant issues From Serguei.Krivov at uvm.edu Mon Aug 9 12:28:47 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Mon, 9 Aug 2004 15:28:47 -0400 Subject: [seek-reports] growl status report Message-ID: <000001c47e47$17d9bd20$3ca6c684@BTS2K3000D5635086B> Progress Report Serguei Krivov 8-09-2004 1) Completed tasks/bugs fixed -GrOWL applet for ESD (90% coding) with stylesheet for configuring icons, labels , and colors -extensive testing of growl rendering and saving to owl and related discussions with Rich -minor bug fixes 2) Current Work and Bugs -finishing applet -datatypes boxes are due 3) Significant issues What datatypes to support in growl? This seems has been settled - support mainly owl-dl recommended datatypes -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040809/c430671e/attachment.htm From rods at ku.edu Mon Aug 9 12:57:26 2004 From: rods at ku.edu (Rod Spears) Date: Mon, 09 Aug 2004 14:57:26 -0500 Subject: [seek-reports] Status 8/2 - 8/6 Message-ID: <4117D726.4080903@ku.edu> Completed Tasks/ Bugs Fixed: * Continued with testing and documenting * Fixed some UI bugs * Worked on KU's Ecogrid server machine (production machine) * Vacation 1.5 days Current Work and Bugs: * Continued on Bug 1595 - Create Advance Query Builder UI Important or Outstanding Issues (of a significant nature) * None Work This Week: * Finish documention for QB * Submit code for code review * Start on Kepler integration -- Rod Spears Biodiversity Research Center University of Kansas 1345 Jayhawk Boulevard Lawrence, KS 66045, USA Tel: 785 864-4082, Fax: 785 864-5335 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040809/cb8e2f73/attachment.htm From tao at nceas.ucsb.edu Mon Aug 9 15:32:12 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Mon, 9 Aug 2004 15:32:12 -0700 (PDT) Subject: [seek-reports] Status report Message-ID: Status Report Jing Tao 08/09/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Query engine against data object in Kepler Significant Issues ------------------ * None -- Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From bzhu at sdsc.edu Mon Aug 9 19:47:25 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 9 Aug 2004 19:47:25 -0700 Subject: [seek-reports] RE: status report from Bing Zhu - Aug 9 In-Reply-To: Message-ID: Completed Tasks/Bugs Fixed: - finalized the gwsdl for ecogrid's put which successfully created stubs, wsdl, etc , for Ecogrid' put. - finished the skeleton implementation of ecogrid's put. - created a client program for ecogrid's put. - test put client and put service to verify that data (binary or metadata data in XML doc) are transferred correctly from client to a remote service Current Work and Bugs: - implementation of uploading files within SRB for Ecogrid's put - implementation of uploading metadata for files in SRB for Ecogrid's put Significant Issues: - none From thau at learningsite.com Wed Aug 11 03:11:19 2004 From: thau at learningsite.com (dave thau) Date: Wed, 11 Aug 2004 03:11:19 -0700 (PDT) Subject: [seek-reports] report for dave thau aug 2 - aug 6 Message-ID: <31102.213.39.30.58.1092219079.squirrel@213.39.30.58> Report for Dave Thau, Aug 2 - Aug 6 (don't know if you're still doing this but... here goes) 1) Completed tasks/bugs fixed Installed LSID server on Kansas machine and mostly integrated it with the current taxon server. 2) Current Work and Bugs Getting the LSID server to return something more interesting than just the name of the concept. Adding code to keep track of who entered concepts and limiting the ability to edit concepts to those who've entered them. 3) Significant issues The "something more interesting" returned by an LSID will depend on work being done over the next few weeks to map seek taxon concepts onto the schema that's being finalized in Napier. It's almost there, and the mapping should be very direct. The LSID server is on a firewalled machine - changes to the Kansas DNS will be necessary to make the server live. The LSID prefix has not been decided. I've registered taxaserver.org, and I recommend the LSIDs look like this: urn:lsid:taxaserver.org:seek:1 Where 1 is the actual concept being requested. I've passed this recommendation onto Jim Beach and Susan Gauch and CCed Dave Vieglais on that. From xianhual at email.unc.edu Mon Aug 16 07:09:58 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 16 Aug 2004 10:09:58 -0400 Subject: [seek-reports] seek report Message-ID: <1092665398.4120c0369286f@webmail0.isis.unc.edu> Status report Xianhua Liu August 16, 2004 Completed Tasks/ Bugs Fixed: -------------------------------------------------------------------- * Designed and partially implemented TaxonomicModel of TCBE * Designed and implemented Java Panel Hierarchy to access data objects contained in the TaxonomicModel Current Work and Bugs: ------------------------------------------------------------------- * Designing and implementing Data Proxy to access data source defined by TaxonomicModel Significant Issues ------------------------------------------------------------------- * ------------------------------------------------------------------- From rgales at eecs.ku.edu Mon Aug 16 11:14:20 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 16 Aug 2004 13:14:20 -0500 Subject: [seek-reports] Status Report 8-9 to 8-13 2004 Message-ID: <4120F97C.3080308@eecs.ku.edu> Status report Robert Gales August 16 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Restructured code packaging, moving the concept and tree packages to a higher level for use between the client and server code (Bug 1646) * Added permanent classes for handling the connection to the SOAP server instead of generating them from WSDL (Bug 1646) * Changed the build process to use Maven (Most of Bug 1648) Current Work and Bugs: ---------------------- * Looking into mechanisms for flexible generation of SQL statements instead of essentially hardcoded statements Significant Issues ------------------ * None From rods at ku.edu Mon Aug 23 11:41:08 2004 From: rods at ku.edu (Rod Spears) Date: Mon, 23 Aug 2004 13:41:08 -0500 Subject: [seek-reports] Status 8/16 - 8/20 Message-ID: <412A3A44.1090805@ku.edu> Completed Tasks/ Bugs Fixed: * Bug 1595 - Create Advance Query Builder UI * Completed taks, Jing checked in the code. Current Work and Bugs: * Continued on Bug 1660 - Add QueryBuilder to the Data Actors Important or Outstanding Issues (of a significant nature) * None Work This Week: * Learn more of Kepler and work on integration From bzhu at sdsc.edu Mon Aug 23 19:05:26 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 23 Aug 2004 19:05:26 -0700 Subject: [seek-reports] status report from Bing Zhu - Aug 16 Message-ID: Completed Tasks/Bugs Fixed: - completed the implementation and test for 'put' service for SRB data management system in Ecogrid. The implementation includes uploading raw data into SRB as datasets and uploading metadata for datasets stored in SRB. Current Work and Bugs: - implementation of Ecogrid's put for Metacat system Significant Issues: - none From bzhu at sdsc.edu Mon Aug 23 19:05:28 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 23 Aug 2004 19:05:28 -0700 Subject: [seek-reports] status report from Bing Zhu - Aug 23 Message-ID: Completed Tasks/Bugs Fixed: - vacation off from Aug 16 to Aug 20 Current Work and Bugs: - implementation of Ecogrid's put for Metacat system Significant Issues: - none From astewart at ku.edu Mon Aug 30 10:35:31 2004 From: astewart at ku.edu (Aimee Stewart) Date: Mon, 30 Aug 2004 12:35:31 -0500 Subject: [seek-reports] Weekly Status Report Message-ID: <41336563.3080204@ku.edu> An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040830/80810ccd/attachment.htm From rgales at eecs.ku.edu Mon Aug 30 14:37:54 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 30 Aug 2004 16:37:54 -0500 Subject: [seek-reports] Status report 8-23-04 to 8-27-04 Message-ID: <41339E32.9090105@eecs.ku.edu> Status report Robert Gales Aug 30, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Bug 1648 - Coding style checks configured - All code fixed to conform to coding style guidlines - The complete site is generated using maven * Added build target to create a client side jar file for use with the LSID server Current Work and Bugs: ---------------------- * Bug 1663 - Create a web-based prototype for demonstrating the API of the SEEK Taxon to the TDWG community Significant Issues ------------------ * None From bzhu at sdsc.edu Mon Aug 30 19:00:31 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 30 Aug 2004 19:00:31 -0700 Subject: [seek-reports] status report from Bing Zhu - Aug 30 Message-ID: Completed Tasks/Bugs Fixed: - getting familiar with Metacat APIs - established initial service skeleton with which tests were done to verify the data byte stream are correctly sent from user side to service side. Current Work and Bugs: - implementation of Ecogrid's put service to upload files in Metacat - implementation of Ecogrid's put service to upload Metadata for Metacat system Significant Issues: - none From rods at ku.edu Tue Aug 31 06:35:37 2004 From: rods at ku.edu (Rod Spears) Date: Tue, 31 Aug 2004 08:35:37 -0500 Subject: [seek-reports] Status 8/23 - 8/27 Message-ID: <41347EA9.7070006@ku.edu> Completed Tasks/ Bugs Fixed: * I got the Query Builder to work with the Eml200DataSource Actor * The QB appears when you right-click and select "Look Inside" Current Work and Bugs: * Bug 1660 - Add QueryBuilder to the Data Actors Important or Outstanding Issues (of a significant nature) * None Work This Week: * Bug 1660