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Etherpad for meeting notes: http://firuta.huh.harvard.edu:9000/FP-2012Apr18


  • Repository reorganization progress
  • Collaborations/Potential Collaborations
    • Specify - Symbiota - FP progress report
  • VM/Appliance Resource offer by iDigBio
  • State of Ecosystem components
    • Firuta configuration.
    • Client helper: Annotation generation.
    • Integration with Morphbank.
    • AnnotationProcessor: Specify Driver.
    • FP Access point API and FP Network Nodes.
  • Pending Tech Issues
    • Packaging Structure
    • API For Query and Cluster Finding
    • Tech group needs to make a decision on or set a date for decision for the query language for pub-sub for Apple Pie.
    • Tech group needs to decide on or set a date for decision for the scope, composition, and implementation of the "global cache."
    • Tech group needs to document the use, roles, and rationales for identifiers.
      • Who is responsible for MessageIDs and what purposes do they serve.
      • Identifiers in messages
      • Identifiers in annotations


  • Paul
    • Georeferenced MCZ IP-100502 to use in example new georeference annotation http://www.etaxonomy.org/ontologies/ao/aod_example_8.rdf.
    • Coordinated edits and got two SPNHC abstracts submitted (DemoCamp of FP and poster on ApplePie).
    • Installed 4Store and librdf on firuta.
    • Drafted network diagrams including OAI-PMH for potential Symbiota-Specify-Morphbank collaboration.
  • Maureen
    • coordinated reorganization of SourceForge repository
    • maven-ized FP-SpecifyDriver and FP-API-Libary projects
    • created git repositories for Morphbank and Symbiota modifications
    • assembled code change requests for Morphbank and Specify
    • installed Archiva on firuta
  • Bob
    • consult with David about RdfBeanHandler
    • discuss Garcia et al. extension proposals to AO
    • setting up GoldenGate project again
  • Lei
    • installed Morphbank and FP-Node on local machine and can successfully launch the annotation into FP-Node from Morphbank with great help from David and Maureen
    • Finished the assignment of svn repository clean, including moving the FP-Mapper into FP-Driver, moving annotation processor and webApp from FP-Network into FP-Access. The code needs to be further cleaned and reorganized after we're clear about the boundary of the projects and develop the other parts of the FP network.
  • David
    • Created Annotation Generation REST webservice and PHP libraries that invoke it and the AccessPoint webservice for use with Morphbank, Symbiota and other clients.
    • Added a rest call to the symbiota new determination form. Symbiota can now inject annotations into fp
    • Deployed the webservice to firuta on fpnode2.
    • Checked in SVN projects to new locations (FP-ClientHelper, FP-Node etc)
    • Installed glassfish on firuta, configured a mysql datasource and the messagestore db for use by AccessPoint.
    • Working on finishing deployment of the AccessPoint to firuta on glassfish.


Filtered Push Team meeting 2012 Apr 18

Present:Bertram, Lei, James, Bob, David, Paul, Maureen


  • Repository reorganization progress

Maureen: Everyone working on getting their projects to their new locations. Third party Morphbank and Symbiota are going to move to the git repository on sourceforge. Workflow for using them is being worked out and will be documented.

Bob: Derived artifiacts, BOUML html, javadocs - agreement they don't belong in SVN. Any of those things that result from a checkout, should have a post-commit maven task to post current versions to the source forge project web site.

Maureen: Totally agree. Hudson will do this. Can test, build, deploy java docs, etc. Worth doing so. Automated pull and build from scripts very valuable. Also have set up archiva maven repository on Firuta.

Discussion: Concur very valuable, Maureen to set up Hudson.

Need to close some ports on firuta at the machine firewall level.

  • Collaborations/Potential Collaborations
    • Specify - Symbiota - FP progress report

Paul: Description of call.

Bob: What is the science question?

Maureen: Workflow sounds like Kepler Curation.

Bertram: Overall sounds reasonable, Kepler as platform, probably needs custom module development.

    • Kepler

Bertram to set up poll to set up a call.

Bob: IDCC folks have a document on Kepler, Bob forwarded to Lei and Bertram for comments.

  • VM/Appliance Resource offer by iDigBio

Paul needs to forward questions to continue discussion to iDigBio contct.


Current target for code freeze for demonstration: 2012-May-29.

All to update current status on Roadmap: http://etaxonomy.org/mw/Roadmap#Current_Status

  • State of Ecosystem components
    • Firuta configuration.

David: Network pieces deploying. Glassfish installed, ready to install node software. Deployed annotation generation code in tomcat. Symbota and morphbank not patched yet.

Node1: glassfish - FP node Node2: tomcat - annotation generation Node3 Node4: Symbiota Node5: Morphbank Node6: Morphbank image server

Maureen: Symbiota installed, has data, Morphbank installed, has data, want to set up scriptable patch process.

Bob: Things to specify: Is deployment architecture going to be everything proxied through port 80? Do we have any requirement of separation of services? Rephrase: Document interaction requirements of multiple clients running on the same machine connecting as clients to a FP node.

Paul: librdf and 4store installed on firuta and available for investigating triplestores.

    • Client helper: Annotation generation.

David: Webservice uses client helper library (with rdfhandler), rest webservice takes xml in domain vocabulary (according to deployed configuration), has php library for invoking this web service, returns rdf/xml annotation, second web service can inject this in an annotation message to FP access point.

    • Integration with Morphbank.
    • Integration with Symbiota

David: Form submission in Symbiota now hooked into client helper web services.

    • AnnotationProcessor: Specify Driver.

Lei: installed FP node on local machine, working on hooking annotation processor back to network.

Need: Annotation processor needs to get messages back from network. Needs implementation of call to access point to retrive messages on arbitrary interest. Need implementation of call to access point to express interest.

Maureen wll coordinate - point Lei at query builder in current web client, coordinate discussion of implementation of expression of interest message and check for messages message in node with David.

Lei: Messaging: Use MySQL implementation.

Paul, yes, but interaction of clients with messaging through FP Node Access Point webservice.

Maureen: Need some mockups of interactions to be shown at SPNHC to guide UI design.

Paul: And we need to get Jim and James involved, and that's the goal of the firuta deployments.

    • FP Access point API and FP Network Nodes.

Ready to deploy ear onto firtua.

Resources configured in glassfish on firuta.