2009Jan15

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Zhimin and Maureen demonstrated a hardwired query seeking all network records with specific given values for two mattributes: collectorNumber and reproductiveState. (Toy data was used for this demo). This was demonstrated on a network with three nodes on three different physical machines at HUH. In the demo, the Hadoop implementations were running on three different machines, of which two shared a common MySQL.

For next meeting 2009Jan22 we hope to have these things done:

  1. Maureen able to map between Specify and a suitable subset of ABCD, wrap it in FP message and launch it. This will be done using specify and is probably adapted from code she already has working to export to XML
  2. Maureen able to map in reverse direction to above, probably based on Rod's CSV import code.
  3. Maureen able to attempt simple Specify Workbench UI to formulate and launch queries for above and report result sets.
  4. Paul to break Specify sample data into 3-4 data sets with some overlap as testbed for deployment on separate nodes (Query ASA to get subset of records, split in four parts with overlap, then import to specify instances via workbench.)
  5. Zhimin assist Maureen as needed, and set up node at umbfp.cs.umb.edu to participate in demo.
  6. Bob and James M grin in encouragement
  7. All other participants and observers applaud wildly

--Bob Morris 14:23, 15 January 2009 (EST)

Preliminary ASA query to get subset of about 300 specimen records:

select barcode,organization.acronym, typestatus.name, col.name as collectorname, collector_no, 
        taxon.fullname, gen_name, taxon.name,
        site.locality, site.latitude_a, site.longitude_a, elev_from, elev_to, h_country_name, h_primary_name, h_secondary_name, h_town_name
from specimen_item left join specimen on specimen_item.specimen_id = specimen.id
   left join organization on specimen.herbarium_id = organization.id
   left join botanist_name col on specimen.collector_id = col.botanist_id
   left join site on specimen.site_id = site.id
   left join geo_unit on site.geo_unit_id = geo_unit.id
   left join type_specimen on specimen.id = type_specimen.specimen_id
   left join st_lookup typestatus on type_specimen.type_status_id = typestatus.id
   left join taxon on type_specimen.taxon_id = taxon.id
   left join h_taxon_lookup on taxon.id = h_taxon_lookup.taxon_id
where barcode > '654515' and barcode < '956915'
   and (col.type_id = 110103 or col.id is null)
   and site.latitude_a is not null
union
select barcode,organization.acronym, 'non type', col.name as collectorname, collector_no, 
        taxon.fullname, gen_name, taxon.name,
        site.locality, site.latitude_a, site.longitude_a, elev_from, elev_to, h_country_name, h_primary_name, h_secondary_name, h_town_name
from specimen_item left join specimen on specimen_item.specimen_id = specimen.id
   left join organization on specimen.herbarium_id = organization.id
   left join botanist_name col on specimen.collector_id = col.botanist_id
   left join site on specimen.site_id = site.id
   left join geo_unit on site.geo_unit_id = geo_unit.id
   left join determination on specimen.id = determination.specimen_id
   left join taxon on determination.taxon_id = taxon.id
   left join h_taxon_lookup on taxon.id = h_taxon_lookup.taxon_id
where barcode > '654515' and barcode < '956915'
   and (col.type_id = 110103 or col.id is null)
   and site.latitude_a is not null;