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As an integrating/translational platform, caIntegrator depends on service-level or API interfaces for several other applications in the caBIG suite of tools. Many of these applications have ongoing development and deploy multiple releases each year. In order to better plan for potential breakage or retest necessary in caIntegrator, the team undertook an analysis of these dependencies and the planned release schedules for each. This document highlights dependencies and serves as a place to discuss any breakage to caIntegrator and to schedule this into an iteration.
Application Dependencies
Note that only differences between the caIntegrator tech stack and the caBIG tech stack are highlighted here. Areas where we are already in compliance are not listed. See the Technology Stack 2010 page for a complete list.
The following applications are used by caIntegrator and require some sort of dependency management. This table will track upcoming releases and any known changes or retest required for these releases. This work can then be scheduled into an upcoming caIntegrator iteration.
Application / Service Technology | caIntegrator | Next 2010 | Projected | Notes/Recommended Resolution Interface Summary / Needed caIntegrator Changes | Planned |
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Container |
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JBoss | 4.0.5 | 5.1.x | 5.1.x | 5.1.x incompatible with Grid as per Grid Compatibility Matrix | none |
Database |
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| MySQL | 5.0.45 | 5.1.x | 5.1.x | Upgrade when feasible or when forced by systems team or by CSM release that only supports 5.1.x.
caArray | 2.4 | 2.5 | TBD | Use Java RMI-based "external model" API | TBD |
NBIA | 4.4 | 4.5 | 10/31/10 | Use caGrid data service for CQL queries and caGrid grid file transfer service | TBD |
AIM | 1.5 | 3.0 | 1/31/11 | Use caGrid data service for CQL queries. Custom serialization/deserialization client used. | TBD |
GenePattern | 3.2.3 | TBD | TBD | caGrid analytical service used for genomic algorithms | TBD |
Bioconductor | TBD | TBD | TBD | caGrid anaytical service for caDNAcopy used for copy number data during study deployment | TBD |
caBio | 4.2 | TBD | TBD | caGrid service used for keyword or pathway based gene search. | TBD | TBD |
CBIIT Internal |
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caGrid | 1.2 | 1.3 | 1.4 | NBIA has already upgraded to 1.3 but has provided us with a backward compatible client (1.2 based) to call their 1.3 service. Any upgrade must also coordinate with Bioconductor (1.2 based), GenePattern (1.2 based), caDSR (?), and caBio (?) as well. | TBD |
CLM | 3.2 | 4.1.x | 4.2.x | Unclear of the impact of this migration. | TBD |
Build & Deploy |
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JDK | 1.5 | 1.6 | 1.6 | JDK 1.5 is end-of-life. Systems has set a June 2011 deadline to upgrade. | TBD |
Ant | 1.7.0 | 1.7.x | 1.8.x | We are already compliant with 2010. We can move to 1.8.x when recommended by BDA. | none |
AnthillPro | 2.6 | 3.x | 3.x | This is no work for the development team other than testing with new AHP server. | TBD |
Subversion | 1.3 | 1.6.x | 1.6.x | We are currently on the GForge SVN server, which is running 1.3. We should migrate to the newer ncisvn SVN server which is on 1.6. This should be no work for the development team other than having to re checkout from the new server when migration is complete and some testing. | TBD |
Dev Libraries |
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Axis | 1.2RC2 | 1.x | 1.x | We are technically compliant here, but GenePattern(?) has shown an interest in upgrading to Axis 1.4. We are locked into the current revision because of the grid. We need to research alternatives to support a possible GenePattern upgrade in the future. | TBD |
Spring Framework | 2.5.6 | 2.5.x | 3.x | We are compliant now. | none |
