sql_io.py: put_table(): Removed no longer applicable requirement that it be run at the beginning of a transaction, which was only required when the output table was locked during the function call
sql_io.py: put_table(): Documented that the function's insert/if not exists get algorithm does not support database triggers that populate fields covered by a unique constraint
inputs/FIA/_src/_README.TXT: Documented that FIA does not provide data for some states, e.g. HI
config/: Set svn:ignore to exclude *password files
Removing config/bien_read_password from version control
Removing config/bien_password from version control
inputs/FIA/: Added refreshed data (not yet mapped)
input.Makefile: Existing maps discovery: $(exts): Also match uppercase versions of extensions
lib/common.Makefile: Added $(ucase) and $(ci)
inputs/FIA/_src/Makefile: Table bundling: $(tableCsvs): Fixed bug where need to replace % with $* in $(csvPattern)
inputs/FIA/_src/Makefile: Table bundling: Fixed bug where need to remove trailing slashes from dirs that will match a target pattern
inputs/FIA/_src/Makefile: Added Table bundling targets to regroup CSVs by tables
lib/common.Makefile: Added $(mkdir)
Added inputs/FIA/_src/_README.TXT with Bob's comments
input.Makefile: SVN: $(_svnFilesGlob): Added README.TXT
mappings/VegCore.csv: Regenerated from wiki. Synonym lists have now been translated to sections to create a web page anchor for each synonym, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore_refactoring#Index-synonyms-as-web-page-anchors>. This enables searching for VegCore synonyms in the data dictionary as well as terms, and makes it possible to swap a term and a synonym while still keeping both as indexed anchors.
mappings/VegCore.csv: Regenerated from wiki. All uncategorized terms have now been moved to tables.
README.TXT: Maintenance: VegCore data dictionary: Added steps to check that no terms were lost when moving terms
inputs/import.stats.xls: Updated import times
mappings/VegCore.csv: Regenerated from wiki
schemas/vegbien.sql: analytical_stem_view: coordinates: Only use county_centroids coordinates when datasource coordinates are not provided, not also when datasource coordinates aren't geovalid. This also fixes a bug where (NULL) county_centroids coordinates were used for non-geovalid coordinates even when there was no county_centroids match, rather than including the non-geovalid coordinates.
schemas/vegbien.sql: taxondetermination: Added is_datasource_current, which is autopopulated to the most recent datasource-provided taxondetermination
schemas/vegbien.sql: taxondetermination: Added taxondetermination_single_accepted_determination unique index to facilitate joining on the accepted determination
schemas/vegbien.sql: taxondetermination: Added taxondetermination_single_matched_determination unique index to facilitate joining on the matched determination
schemas/vegbien.sql: taxondetermination: Removed notespublic, notesmgt, which are not used by VegBIEN
schemas/vegbien.sql: taxon_trait_view: scientificName: Use taxonverbatim.taxonname when taxonlabel/taxonverbatim.taxonomicname are not provided, to accommodate TNRS names. This is part of the workaround for the bug where the taxonlabel's taxonomicname (concatenated taxonomicname) is occasionally not populated.
schemas/vegbien.sql: taxon_trait_view: Added workaround for bug where the taxonlabel's taxonomicname (concatenated taxonomicname) is occasionally not populated due to a taxonlabel constraint violation, by using the taxonverbatim's taxonomicname instead in these cases. This bug, which appeared in the r7317 import, is so far not reproducible (tested on Mac OS X), so its cause is unknown, but may be caused by a bug in functions._merge_prefix(), which is run on the taxonlabel's taxonomicname but not the taxonverbatim's taxonomicname.
schemas/vegbien.sql: analytical_stem_view: Added dateIdentified, identificationRemarks per Brad's request (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#E-mail-on-2013-1-16)
inputs/FIA/_src/Makefile: Added extraction targets to extract zip archives
inputs/FIA/_src/download: Use new Makefile, which uses make logic to determine if a file needs to be downloaded
Added inputs/FIA/_src/Makefile, with targets to download each zip archive
schemas/vegbien.sql: analytical_stem_view: derived terms: Added _bien suffix per Brad's request (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#Brad-Boyles-comments)
Added inputs/FIA/_src/FIADB_version4.accdb.url
inputs/FIA/_src/download: Only run wget on files that don't yet exist
inputs/FIA/_src/download: Run wget in same directory as script to ensure files get downloaded there
inputs/FIA/_src/download: Set svn:executable
Added inputs/FIA/_src/download to download archives of CSVs for each state
to_do/timeline.2013.xls: Updated with changes during conference call
schemas/vegbien.sql: taxon_trait_view: Renamed datasource_taxonverbatim to taxonverbatim because there is now only one taxonverbatim
schemas/vegbien.sql: taxon_trait_view: Moved the taxondetermination.iscurrent filter to the join condition to allow using the taxondetermination_single_current_determination index
schemas/vegbien.sql: taxon_trait_view: Join only on the primary taxonlabel, not the accepted taxonlabel, because the scrubbed name is now available directly via the taxonlabel attached to the scrubbed taxondetermination
schemas/vegbien.sql: analytical_stem_view: Added locality
inputs/UNCC/Specimen/map.csv: accession: Remapped to catalogNumber per Bob's corrections
schemas/vegbien.ERD.mwb: Regenerated exports
README.TXT: Schema changes: Added instructions to run the appropriate sync function when changing the analytical views
schemas/vegbien.sql: analytical_stem_view: Added georeferenceProtocol, which is set to 'county centroid' when county centroid coordinates are used
make_analytical_db: Don't run export_analytical_db if the SQL script exits with an error
README.TXT: Full database import: record the import times in inputs/import.stats.xls: Added `export version=<version>` because import_times may be run in a shell different from the one that the import was run in
schemas/vegbien.sql: taxonverbatim: taxonverbatim_unique: Added morphoname for cases when there is just a morphoname, and to distinguish taxonverbatims with the same taxonlabel but different morphonames
schemas/vegbien.sql: stemobservation: Added stemobservation_non_empty CHECK constraint to prevent creating an empty stemobservation for plantobservation rows without stem data but with stem mappings
schemas/vegbien.sql: taxonverbatim: Allow taxonlabel_id to be NULL when morphoname is provided
schemas/vegbien.sql: taxonverbatim: Added source_id to allow creating taxonverbatims without a (scoping) taxonlabel
schemas/vegbien.sql: analytical_stem_view: Removed speciesBinomialWithMorphospecies now that it's duplicated by scientificNameWithMorphospecies
schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Create it using the speciesBinomialWithMorphospecies formula, per Brad's request at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#2013-1-18>
schemas/vegbien.sql: analytical_stem_view: Added coordinateSource to indicate whether coordinates are from county_centroids (georeferencing) or the source data
schemas/vegbien.sql: Added coordinatesource enum
schemas/vegbien.sql: analytical_stem_view: coordinates: Also use the county_centroids coordinates when the datasource coordinates are not geovalid. (Note that canon_place.geovalid will be NULL, i.e. not true, when the datasource coordinates are NULL.)
schemas/vegbien.sql: scientificName: Set to taxonverbatim.taxonname instead per Brad's changes at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#2013-1-18>. Renamed to taxonName since this now doesn't include the author, which is part of DwC's scientificName field.
schemas/vegbien.sql: sync_analytical_stem_to_view(): Support running the function when dependent views do not exist. This allows using the sync function when changing column names of the analytical_stem_view, which sometimes requires manually dropping and re-creating the analytical_aggregate_view.
backups/Makefile: %.md5/test: Added comment to run with `make -s` to avoid echoing make commands
README.TXT: Full database import: Added steps to scrub unscrubbed taxondeterminations (if they are not scrubbed automatically)
inputs/.geoscrub/_src/README.TXT: Added e-mails from Jim about how the county_centroids data was generated
schemas/vegbien.sql: analytical_stem_view: coordinates: Use new county_centroids coordinates and uncertainty when the datasource's coordinates are not available
Added inputs/.geoscrub/county_centroids/ from Jim
inputs/.geoscrub/import_order.txt: Added geoscrub_output
README.TXT: Full database import: In PostgreSQL: Added step to check that there are TNRS taxondeterminations
README.TXT: Full database import: In PostgreSQL: Added step to check that unscrubbed_taxondetermination_view returns no rows
Added inputs/newWorld/newWorldCountries/_no_import
to_do/timeline.2013.xls: Updated with Brad's modifications
Added inputs/FIA/_src/FIA_summary.b-e.00079.pdf from Bob
Added inputs/.herbaria/_archive/
inputs/.herbaria/: Removed no longer needed geoscrub.*.sql, which has been replaced with bien3_adb.*.sql
inputs/.herbaria/: Removed no longer needed herbaria/. Use ih/ instead.
Added inputs/.herbaria/ih/ and corresponding bien3_adb MySQL export
mappings/VegCore-VegBIEN.csv: Don't create NCBI crosslinks for the matched taxonomic name. These crosslinks are no longer needed now that TNRS provides a separate accepted name on which crosslinks can be made.
schemas/vegbien.sql: unscrubbed_taxondetermination_view: Include the accepted name's row next to the matched name's row instead of merging the two together into one TNRS row, to allow including separate taxondeterminations for the matched and accepted names. Added Max_score from TNRS.tnrs.
schemas/vegbien.sql: taxondetermination_set_iscurrent(): Added new determinationtype accepted to sort order
mappings/VegCore-VegBIEN.csv: Mapped accepted* taxonomic name, now to separate accepted taxondetermination
schemas/vegbien.sql: taxondetermination_set_iscurrent(): Changed TNRS determinationtype from computer to matched, to allow for a separate accepted determinationtype
schemas/vegbien.sql: taxonlabel: Removed creationdate, which duplicates taxondetermination.determinationdate
schemas/vegbien.sql: analytical_stem_view: isNewWorld: Removed no longer needed COALESCE to false, because newWorldCountries now uses false where applicable instead of NULL. This also ensures that isNewWorld will be NULL if there is no country name to test, which was not the case in the previous workaround.
Added inputs/newWorld/newWorldCountries/ with postprocess.sql that sets isNewWorld to false wherever it's NULL. (The input table only marks New World countries as true, but doesn't mark non-New World countries as false.)
schemas/vegbien.sql: analytical_stem_view: isNewWorld: Fixed bug where need to COALESCE "newWorldCountries"."isNewWorld" to false, because it is only set to a boolean for countries that are New World
README.TXT: Full database import: freeing disk space: Updated import schema size, which is smaller due to the removed CTFS staging tables, removed duplicate rows, and possibly fewer index holes
README.TXT: Full database import: After running `make schemas/$version/publish`, added `unset version` to make sure future version-dependent commands use the public schema
schemas/vegbien.sql: taxon_trait_view: Fixed bug where measurementUnit needed to be set to trait.units, not name
schemas/vegbien.sql: provider_count_view: Don't set default values for sourcetype/observationtype, because the appropriate values are now set for all top-level inputs and these defaults are not applicable for data owners not in geoscrub.herbaria
inputs/bien2_traits/Source/map.csv: Mapped observationType
schemas/vegbien.sql: taxondetermination: Removed taxondetermination_computer_min_fit CHECK constraint, whose functionality is now duplicated by unscrubbed_taxondetermination_view's Max_score filter condition. The score threshold value should only be maintained in one place, namely unscrubbed_taxondetermination_view.
schemas/vegbien.sql: unscrubbed_taxondetermination_view: Fixed bug where need to filter out any names that will be rejected by taxondetermination's constraints, because otherwise, these names will stay in unscrubbed_taxondetermination_view and be repeatedly reimported
