Science Environment for Ecological Knowledge
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Science Environment for Ecological Knowledge









 

 

 



KU Taxon Update_Sept 2005

Difference between version 8 and version 4:

Line 4 was replaced by line 4
- * Found that it could be done using Apache's BCEL library
+ ** Found that it could be done using Apache's BCEL library
Line 6 was replaced by line 6
- * Determined that it would not be useful to have the Web
+ ** Determined that it would not be useful to have the Web
Lines 12-26 were replaced by lines 12-17
- * After discussing it with Matt, it was decided the best route
- to go would be to add the API methods for the ENM use case
- in a manner that the used simple Java types or arrays of them
- * The WSDL was changed to add the necessary API functions
- * The old SOAP interface layer was tossed out and redesigned
- and redeveloped to completely isolate it from the business
- logic
- - Involved creating adapter classes for the concept
- objects to ensure that Java collection objects are
- serialized as arrays
- - Adding an additional class to manage the interface
- between the business logic layer, which has fewer
- API methods all of which use complex objects
- and the SOAP layer
- - Modification of the client side code
+ * After discussing it with Matt, it was decided the best route to go would be to add the API methods for the ENM use case in a manner that the used simple Java types or arrays of them
+ ** The WSDL was changed to add the necessary API functions
+ ** The old SOAP interface layer was tossed out and redesigned and redeveloped to completely isolate it from the business logic
+ *** Involved creating adapter classes for the concept objects to ensure that Java collection objects are serialized as arrays
+ *** Adding an additional class to manage the interface between the business logic layer, which has fewer API methods all of which use complex objects and the SOAP layer
+ *** Modification of the client side code
Line 28 was replaced by line 19
- - A couple of the new API methods needed graph like methods
+ * A couple of the new API methods needed graph like methods
Line 30 was replaced by line 21
- * Node/Edge/Graph classes were created that add all edges
+ ** Node/Edge/Graph classes were created that add all edges
Lines 32-34 were replaced by lines 23-25
- level was created
- * Hibernate mappings to those classes where created
- * Added back to the system the idea of an authoritative list
+ level was created
+ ** Hibernate mappings to those classes where created
+ ** Added back to the system the idea of an authoritative list
Line 36 was replaced by line 27
- - Modified the object model at the same time to more simply handle
+ * Modified the object model at the same time to more simply handle
Line 38 was replaced by line 29
- * modified business code, database mappings and code
+ ** modified business code, database mappings and code
Line 40 was replaced by line 31
- - Added an n-gram matching algorithm to implement a dictionary for
+ * Added an n-gram matching algorithm to implement a dictionary for
Lines 46-47 were replaced by lines 37-38
- - Added implementations of the following API methods:
- * getAuthoritativeList: returns all concepts at a particular
+ * Added implementations of the following API methods:
+ ** getAuthoritativeList: returns all concepts at a particular
Line 49 was replaced by line 40
- * getSynonymousNames: returns the list of all synonymous
+ ** getSynonymousNames: returns the list of all synonymous
Line 51 was replaced by line 42
- * getHigherTaxon: returns the a higher taxon at a
+ ** getHigherTaxon: returns the a higher taxon at a
Line 54 was replaced by line 45
- * getBestConcept: returns a list (of hopefully only 1) concept
+ ** getBestConcept: returns a list (of hopefully only 1) concept
Lines 58-59 were replaced by lines 49-50
- - Modifications to the build process
- * War file generation of the SOAP service for easier
+ * Modifications to the build process
+ ** War file generation of the SOAP service for easier
Line 61 was replaced by line 52
- * Automatic generation of Java class files containing the
+ ** Automatic generation of Java class files containing the
Line 64 was replaced by line 55
- - Wrote a harvester for ITIS data that takes in a root TSN and
+ * Wrote a harvester for ITIS data that takes in a root TSN and
Line 67 was replaced by line 58
- * Parses an ITIS XML instance using XPath to generate concepts
+ ** Parses an ITIS XML instance using XPath to generate concepts
Line 70 was replaced by line 61
- * Incorporated tests for this
+ ** Incorporated tests for this
Line 76 was replaced by line 67
- - Wrote a generic import tool that takes in any instance of the TCS
+ * Wrote a generic import tool that takes in any instance of the TCS
Line 78 was replaced by line 69
- * Change in the way that the unmarshalling works sot it uses a
+ ** Change in the way that the unmarshalling works sot it uses a
Line 80 was replaced by line 71
- * Numerous bugfixes to the 0.88b and 0.95.3
+ ** Numerous bugfixes to the 0.88b and 0.95.3
Line 83 was replaced by line 74
- - Modified the TOS to use the Spring framework to configure the
+ * Modified the TOS to use the Spring framework to configure the
Lines 87-90 were replaced by lines 78-82
- - Met with CIPRES project in San Diego and agreed on several
- opportunities for collaboration
- 1. Data
- * both projects are creating XML schemas CIPRes for the
+ * Hibernate training to tune TOS performance
+
+ !!CIPRes Collaboration update
+ * Data
+ ** both projects are creating XML schemas CIPRes for the
Line 92 was replaced by line 84
- * CIPRes could adopt taxonomic model requirements from SEEK
+ *** CIPRes could adopt taxonomic model requirements from SEEK
Line 96 was replaced by line 88
- * SEEK could accept CIPRes recommendations for incorporating sequence
+ *** SEEK could accept CIPRes recommendations for incorporating sequence
Lines 99-100 were replaced by lines 91-92
- * CIPRes must create an archival db, seek need not
- * CIPRes could develop and implement archival Treebase repository
+ ** CIPRes must create an archival db, seek need not
+ *** CIPRes could develop and implement archival Treebase repository
Lines 102-103 were replaced by lines 94-95
- * Saves resources and expands user base on both projects
- * Jenny Wang (SEEK) and Rami Rifaieh (SDSC ontology) could meet to work
+ *** Saves resources and expands user base on both projects
+ *** Jenny Wang (SEEK) and Rami Rifaieh (SDSC ontology) could meet to work
Lines 105-106 were replaced by lines 97-99
- * Formal gathering to merge requirements
- 2. CIPRes may be able to improve and adapt SEEK tools for CIPRes and other
+ *** Formal gathering to merge requirements
+
+ ** CIPRes may be able to improve and adapt SEEK tools for CIPRes and other
Lines 108-118 were replaced by lines 101-102
- * adopt SCIA (schema matching tool)
- * create workflow functionalities in Kepler
- 3. Interface
- * SEEK - Usability
- * CIPRes - dynamic interface generation and user configuration based
- on PISE strategy
- 4. Visualization
- * CIPRes involved in tree visualization, but no deticated people on it
- now, can they help SEEK?
-
- - Hibernate training to tune TOS performance
+ *** adopt SCIA (schema matching tool)
+ *** create workflow functionalities in Kepler
Line 120 was replaced by lines 104-107
-
+ ** Interface
+ *** SEEK - Usability
+ *** CIPRes - dynamic interface generation and user configuration based
+ on PISE strategy
At line 121 added 3 lines.
+ ** Visualization
+ *** CIPRes involved in tree visualization, but no deticated people on it
+ now, can they help SEEK?

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