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Etherpad for meeting notes: http://firuta.huh.harvard.edu:9000/FP-2012May09


  • NSF Annual Report
  • Collaborations
    • CNH
    • SCAN
        • SCAN IT meeting, 14 August; SCAN general meeting, 15-16 August. Both are in Tempe. JH will attend IT meeting and first morning of general meeting. Someone else from FP (Paul?) should attend both meetings.
    • ABI proposal with Wisconsin and KU.
  • SPNHC demo mockups


  • Paul
    • For MCZ, started extending Kepler curation package to use GBIF's checklist bank API.
  • Maureen
    • Loaded HUH sample collections data into Symbiota on firuta; established an upload procedure for importing data from a Specify database into a Symbiota collection.
    • Loaded 2 specific additional sample records into Symbiota, Morphbank, and Specify on firuta
    • Extended a sample OAuth provider to authenticate to a Specify database
    • Implemented a demonstration OAuth client to use the Specify OAuth provider, as an example of how the mapper can obtain authorization to update a Specify database on behalf of a web user who has Specify credentials


Filtered Push Team Meeting 2012 May 09

Present: Maureen, David, Bertram, James, Heather Cole, Lei, Jim, Bob.


  • NSF Annual Report

Jim: Sent out google doc with template and data from last year, have until end of July to fill in. Please add in information, priority after SPNHC.

  • Collaborations
    • CNH

Discussion, target discussions with Patrick/Chuck after SPNHC.

Start date? July 1? Need to find out.

    • SCAN
        • SCAN IT meeting, 14 August; SCAN general meeting, 15-16 August. Both are in Tempe. JH will attend IT meeting and first morning of general meeting. Someone else from FP (Paul?) should attend both meetings.

Paul to attend both. JH as above.

    • ABI proposal with Wisconsin and KU.

Call this morning. Narrowing on smaller scope.

Jim: Background, Corrina invited us to discuss with Symbiota and Specify. Regular calls in last few weeks. Work involved and costs not yet clearly defined yet. Todo from today's call is a document to help refine scope of work from each project.

Bob: Lots of conversation about GUIDs, people need to be reminded that uniquness constraints on GUIDs allow multiple GUIDs for the same objects...

    • Kurator

Bertram: Need to provide paragraph in day or two.

James: Spent some time this morning working on it.

Paul: Taking a shot at extending kurator to be able to use GBIF's checklist bank API.

  • SPNHC demo mockups

Lei: Working up UI following the mockups, very close to ready. Need to work with Maureen to use Driver to get data into Specify.

Maureen: Driver, Created an OAUTH provider for specify, so a client can use the OAUTH provider to grant access to the specify database without the user having to provide their credentials to the mapper. Driver can write into specify with rights of user. Given adequete information, driver can either link to existing data (e.g. by collection object id), or create new records (new determination, new taxon). Will need more information than provided in annotation to create new taxon records.

Lei: Need to better understand API of driver for authentication, query, and push into databse as used by annotation processor.

Google code site with Dave Remson's code for taxon name string parsing/atomization: https://code.google.com/p/taxon-name-processing/

Process: Authenticate into annotation processor, authenticate into oauth service for specify, review (lookup collection object id and existing DwC record), accept annotation, auto parse scientific name into component parts, look up taxonid, if not found, provide user interface to add/confirm information (parent, rank, etc) to link into existing tree, then pass into driver to push into database.

Need mockup of UI for adding a new taxon.

Maureen and Lei to work together on integrating driver and annotation processor to deploy for Jim and James.

David: Symbiota and Specify can submit new determinations as annotations. Can work on having response annotations visible in Symbiota. Register interest is working, Query message to retrieve response annotation history in progress. Partly deployed on firuta, needs to redeploy with Hudson.

Bob: Recursive dialog of annotation, response annotations, responses to those annotations, etc probably needs to go onto table. Query arbitrary depth tree starting only with root.

Lei: How to deploy annotation processor?

Maureen: TODO: will work out how to deploy the war file into tomcat using Hudson.

Paul: Will also need appropriate apache configuration for path to make visible with htaccess control on fpnode2.

Lei: also need access to MySQL.

Maureen: will set up to make this happen.

  • Poster on ApplePie

James: We need to make this. We need to decide what to show in it. Doesn't need to go too deep for this crowd.

James: TODO: Brief outline of narrative for poster by end of week.