| 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? |
