VegRef/.htaccess: URL resolution: mod_rewrite: Fixed bug where also need to consider if %{REQUEST_FILENAME} is a dir or symlink, which occurs e.g. when redirecting to the VegRef/ dir itself

web/VegRef/.htaccess: Turned off RewriteEngine temporarily because it was preventing the internal VegRef redirection from working

Added web/VegRef/, which provides a URL-shortening service for vegetation references. VegRef URLs are short and human-readable enough to be used as database column names. This also causes Google spreadsheets to display a clickable link for each column name, which takes the user to the data dictionary definition for the term. String row IDs (such as global IDs <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs&gt;) can also be clickable VegRef URLs.

inputs/NCU/Specimen/map.csv: cultivated: Map false (0) to NULL because cultivated can only be true or NULL, not false

inputs/CTFS/_src/_README.TXT: Added e-mails from Brad Boyle about issues with species aggregation methods

inputs/UNCC/Specimen/map.csv: Populated specimenHolderInstitutions

Added planning/goals/BIEN3_derived_data_products.docx.url

Added planning/goals/BIEN3_derived_data_products.docx

inputs/ARIZ/omoccurrences/map.csv: cultivationStatus: Map to NULL if it's false, because cultivated can only be true or NULL

schemas/vegbien.sql: analytical_stem_view: Merged taxonName_verbatim and scientificNameAuthorship_verbatim into scientificName_verbatim

schemas/vegbien.sql: analytical_plot: Added specimens fields at the end, for use by plots data that also tracks specimens (e.g. Madidi, SALVIAS)

README.TXT: Full database import: In PostgreSQL: Removed tests related to unscrubbed_taxondetermination_view and TNRS taxondeterminations, which are no longer needed because TNRS is joined directly to analytical_stem_view

mappings/VegCore.htm: Regenerated from wiki. Renamed specimenDonor to specimenDonorInstitution to clarify that this is an institution, not a collector.

inputs/UNCC/Specimen/map.csv: Mapped flower, fruit -> reproductiveCondition using translation is from e-mail conv between Jim Matthews at Habitat Assessment and Bob Peet on 2010-12-2~3

make_analytical_db: Support the $log flag, which toggles output to the terminal or a log file

inputs/import.stats.xls: Updated import times. The core import time has dropped by more than half (!) to ~12 hours, now that the TNRS scrubbing is added using a simple LEFT JOIN, instead of being pushed through the normalized schema. Not since October has the import been this fast!

import_times: When there are no matching logs, exit with status 0 instead of 1 because this is a normal condition

import_times: Fixed bug where sed would wait for user input from stdin when there were no matching logs

README.TXT: Full database import: record the import times in inputs/import.stats.xls: If the row counts do not match up: Added step to get the datasource names from the log file footers

inputs/UNCC/Specimen/map.csv: cultivated: assume anything non-NULL to be cultivated, so that we err on the side of excluding possibly-cultivated specimens

inputs/UNCC/_src/_README.TXT: Added e-mail conv between Jim Matthews at Habitat Assessment and Bob Peet about the meanings of the Leaf, Flower, Fruit, and Root codes

README.TXT: Full database import: Added steps to manually back up the DB. (These steps are specific to the import process, and include filters to exclude previous imports. There are also general backup steps in the Backups > Full DB section.)

inputs/ACAD/Specimen/map.csv: institutionCode: Replace "Acadia University" with the IH code ACAD

inputs/.TNRS/data.sql: Re-ran TNRS on the test_taxonomic_names so that the sample data would contain all the accepted names under the current acceptedScientificName formula, and would not produce any entries for unscrubbed names in tnrs_input_name

schemas/vegbien.sql: tnrs_input_name: taxonlabel.taxonomicname subquery: Don't exclude taxonlabels with a matched_label_id, because matched_label_id is no longer used to indicate that a name has a scrubbed name (this was used when all of TNRS was imported at the beginning of the import)

schemas/vegbien.sql: tnrs_input_name: accepted_name subquery: Renamed to the VegCore table name AcceptedTaxon

schemas/vegbien.sql: tnrs_input_name: taxonlabel.taxonomicname subquery: Use new MatchedTaxon view, which use VegCore column names where possible

schemas/vegbien.sql: tnrs_input_name: accepted_name subquery: Use new MatchedTaxon, AcceptedTaxon views, which use VegCore column names where possible

README.TXT: Full database import: Added instructions to run TNRS and view the TNRS log

README.TXT: Full database import: Removed no longer necessary command to scrub unscrubbed taxondeterminations

*.sql: concat_ws() calls: Fixed bug where need to surround it with NULLIF because concat_ws() returns '' instead of the required NULL when supplied with only NULL args

schemas/vegbien.sql: analytical_stem_view: concat_ws() calls: Fixed bug where arguments were still enclosed in ARRAY[], because the name had been changed from concat_delim() but PostgreSQL removed the VARIADIC keyword without also removing the ARRAY[] wrapper

schemas/vegbien.sql: Removed no longer needed unscrubbed_taxondetermination_view. Use taxonlabel joined to ScrubbedTaxon instead.

inputs/.TNRS/schema.sql: ScrubbedTaxon: Include only matches with a match score of at least 0.8 (score_ok())

inputs/.TNRS/schema.sql: Added back score_ok() and tnrs.tnrs_score_ok index

*.sql: Replaced concat_delim() with concat_ws(), which is built-in as of PostgreSQL 9.1 (http://stackoverflow.com/questions/1943433/postgresql-concat-ws-like-function)

inputs/U/Specimen/map.csv: Populated specimenHolderInstitutions

mappings/VegCore.htm: Regenerated from wiki. Renamed specimenHolders to specimenHolderInstitutions to make it obvious that this is a list of institutions, such as would be in institutionCode in a DwC export.

inputs/SpeciesLink/Specimen/map.csv: Fixed embedded line endings

inputs/NY/Ecatalog_all/map.csv: PlantFungDescription->occurrenceRemarks: Removed "plant fungus" label because this field actually contains the specimenDescription

inputs/.TNRS/import_order.txt: Removed public.unscrubbed_taxondetermination_view

inputs/.TNRS/: Moved no longer needed public.unscrubbed_taxondetermination_view/ to _archive/

root Makefile: Datasources: scrub: Removed no longer needed scrub-remake, which has been replaced by direct use of TNRS.ScrubbedTaxon

schemas/vegbien.sql: analytical_stem_view: taxondetermination: Fixed bug where need to include only the is_datasource_current taxondetermination

schemas/vegbien.sql: analytical_stem_view: Use new TNRS.ScrubbedTaxon directly instead of the scrubbed taxondeterminations added to the normalized DB

inputs/.TNRS/schema.sql: MatchedTaxon: Renamed matchedTaxonomicStatus to preferred name taxonomicStatus

mappings/VegCore.htm: Regenerated from wiki. Taxon: Moved scrubbing-related terms to MatchedTaxon.

inputs/.TNRS/schema.sql: Added matched* prefix where needed

inputs/.TNRS/schema.sql: MatchedTaxon: Added missing Name_submitted column

inputs/.TNRS/schema.sql: MatchedTaxon: Name_matched: Fixed mapping to matchedTaxonName

inputs/.TNRS/schema.sql: MatchedTaxon: Fixed bug where can't map Source to source because it refers just to the source of the matched name, rather than of the record (which would be TNRS itself)

inputs/.TNRS/schema.sql: tnrs_populate_derived_fields(): Use new concat_delim()

schemas/functions.sql: _join*(): Use new concat_delim()

schemas/functions.sql: Added concat_delim() (also in public, but this copy is for use by the functions schema)

inputs/.TNRS/schema.sql: Removed no longer used tnrs+accepted. Use ScrubbedTaxon instead.

inputs/.TNRS/schema.sql: Added MatchedTaxon, AcceptedTaxon, ScrubbedTaxon views, which rename the columns to VegCore names

Removed inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump*, which has been replaced by GBIFPortalDB-2013-02-20.dump

mappings/VegCore.htm: Regenerated from wiki. Renamed MatchedTaxonDetermination/AcceptedTaxonDetermination to MatchedTaxon/AcceptedTaxon because they relate to a taxon name rather than to an application of that name to a TaxonOccurrence

schemas/functions.sql: functions._map(): Made function STRICT because it always returns NULL if either argument is NULL

inputs/UNCC/Specimen/map.csv: campus: Mapped to cultivated, interpreting non-NULL values as true

inputs/UNCC/Specimen/map.csv: campus: Removed mapping to occurrenceRemarks because this is just a code, not a description. Added definition from Bob's validation comments.

inputs/UNCC/Specimen/map.csv: accession: Removed comment that this is actually the catalogNumber, because they are now synonyms

mappings/VegCore.htm: Regenerated from wiki. Split specimenIndexer into specimenStampingInstitution and specimenDonor (which are often the same).

mappings/VegCore-VegBIEN.csv: Removed specimenIndexer->institutionCode mappings because the institutionCode should refer only to the specimenHolder

Added inputs/GBIF/_src/GBIFPortalDB-2013-02-20.dump.gz (a new download they posted to the FTP site)

schemas/vegbien.sql: analytical_specimen: Removed growthForm, threatened_bien at Brad's request (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#UNCC > Brad Boyle's comments > growthForm, threatened_bien)

inputs/UNCC/Specimen/map.csv: Removed mappings to reproductiveCondition because we don't know what the single-letter codes mean

inputs/UNCC/Specimen/map.csv: Fixed embedded line endings

schemas/vegbien.sql: _locationnarrative_is_cultivated(): Fixed bug where need to use NULL instead of false (and bool_or() instead of OR) for a non-match, because the absence of a match doesn't mean it's not cultivated

mappings/VegCore.htm: Regenerated from wiki. Editing: Changed ambiguous terms templates to list the name of the alternative itself in the alternatives list, instead of the ambiguous term + a source suffix. This avoids the need to choose a source suffix for each alternative of an ambiguous term, as the ambiguous term itself (without the suffix) can be listed as the synonym. Coordinates: Disambiguated verbatimCoordinateSystem.

mappings/Makefile: VegCore.thesaurus.csv: `uniq`ify the map after applying initial translations, to support mappings that appear twice (once as the result of an alternative's synonym entry and again as the result of an ambiguous term's alternatives listing)

schemas/vegbien.sql: analytical_stem_view: Added temperature_C, precipitation_m for possible use in John Wiens' plant climatic niche evolution project ("how fast is the rate of climatic niche evolution among species compared to projected changes in climate over the next 100 years? How do these rates compare for temperature and precipitation variables?")

mappings/VegCore.htm: Regenerated from wiki. Added specimenDescription.

mappings/VegCore.htm: Regenerated from wiki. Split apart identificationQualifier and taxonFit. Split apart taxonConfidence and identificationVerificationStatus. Moved identificationQualifier to new QualifiedTaxonName table.

README.TXT: Full database import: To view progress: Use tail -100 to show more of the log files, and not tail -f to avoid blocking when the user just wants to check the status

inputs/BRIT/specimen_flat/map.csv: Only map Notes_Plant to occurrenceRemarks if there is a separate Locality_Description, in order to filter out Notes_Plant values that concatenate everything together (often including a herbarium name that would mess up the cultivated flag parsing)

my2pg.data: Replace \0 (with the backslash) with 0 because \0 isn't allowed in UTF-8

root Makefile: VegBIEN DB: mk_db: Added command to import arbitrary DB users from a config file

inputs/import.stats.xls: Updated import times

inputs/TEX/Specimen2/map.csv: _join() PLANT DATA and MISC NOTES to form occurrenceRemarks instead of _alt()ing them

inputs/TEX/Specimen2/test.xml.ref: Accepted test

inputs/BRIT/_MySQL/MySQL.*.sql.make: Include all tables, not just specimen_flat

my2pg: Replace tinytext, mediumtext with text

Added inputs/GBIF/_src/_README.TXT with Brad's GBIF filtering rules

inputs/FIA/TREE/postprocess.sql: Use :table instead of hardcoding the table name

inputs/FIA/*/postprocess.sql: UNIQUE constraint: Added UNITCD because although it may not be needed to scope PLOT, it is present in all the core tables and thus must be part of the joins' USING columns

inputs/FIA/*/postprocess.sql for core tables: Added unique constraint on the datasource's primary key fields

Added inputs/CTFS/AggregateObservation/ from BIEN2 data

inputs/CTFS/: Switched global _no_import to table-specific _no_imports to allow adding new tables that are imported

Added schemas/TAPIR/SpeciesLink.tapir_request.txt symlink

Added inputs/SpeciesLink/_src/tapir_request.txt

Added schemas/TAPIR/

Added planning/use_cases/rare_species.png

Added planning/goals/BIEN deliverables.png

Added planning/resources/iPlant_Overview_BIEN_2011.pdf.url

planning/goals/Enquist_BIEN_Overview_2011.pptx: Replaced with .url file. Note that the Plone site <http://groups.nceas.ucsb.edu/bien/meetings> is not searchable by document filename.

Added planning/workflow/Boyle_BIEN_data_quality.pdf.url

Added planning/goals/BIEN_Science_2011.pptx.url, BIEN-Tech-Oct2011.ppt.url, Enquist_BIEN_Overview_2011.pptx

Added schemas/VegX/run.py

Added schemas/VegBIEN/growth_forms/Barbara_Dobrin.parsing.scripts/