bugfix: added nodes/_no_import, because the NCBI import doesn't work due to a Postgres 9.3 bug (#859). _no_import used to not be needed because we didn't import the hidden sources.
inputs/.TNRS/Source/map.csv: datasetURL: updated to indicate that this uses the TNRS dev server (the actual URL is private)
fix: inputs/VASCAN/Source/map.csv: observationGranularity should not be specimen because this datasource contains only taxa
fix: inputs/.geoscrub/geoscrub_output/: added _no_import because these tables are metadata that is used in the analytical DB. this is better than relying on bin/import_all not to import these.
fix: inputs/IUCN/: renamed to inputs/.IUCN/ (see issue #940)
fix: inputs/newWorld/: renamed to inputs/.newWorld/ (see issue #940)
bugfix: inputs/IRMNG/: renamed to inputs/.IRMNG/ so that this comes before TNRS, which depends on it (this is a metadata datasource, so it can start with "."). part of issue #940.
inputs/GBIF/_MySQL/.rsync_ignore: don't exclude GBIFPortalDB-*.data.sql.gz, even though this is an intermediate file, because it's better to have a backup of it locally. this was excluded in r13316 (2014-4-24) to free up disk space on the local machine.
fix: inputs/Madidi/LocationObservation/postprocess.sql: parse Spanish dates
fix: mappings/VegCore-VegBIEN.csv: mapped DwC year/month/day, which are split-date alternatives to eventDate. this fixes the missing eventDate in FIA.
bugfix: inputs/FIA/*/VegBIEN.csv: regenerated, replacing these with symlinks to the file used by new-style import
inputs/FIA/taxon_observation.**/test.xml.ref: updated
inputs/FIA/TREE/test.xml.ref: updated
inputs/FIA/REF_RESEARCH_STATION/test.xml.ref: updated
fix: inputs/bien2_traits/TraitObservation/map.csv: mapped VisitingDate to eventDate
fix: inputs/Madidi/LocationObservation/postprocess.sql: populated missing eventDate from PlotInventoryName (authorEventCode)
removed no longer needed inputs/.TNRS/grants.sql, since the grants in schema.sql are now being run
bugfix: inputs/input.Makefile: sql/install: schema.sql should not be passed through pg_dump_limit because it contains GRANT statements that need to be run
inputs/publishable datasources.xlsx: updated
inputs/.TNRS/schema.sql: matchedFamily: just use Name_matched_accepted_family, because TNRS has now been reloaded so that the names that were missing this have it populated
inputs/.TNRS/schema.sql: taxon_match: taxon_match__valid_match: replaced with taxon_best_match__valid_match, which also applies taxon_best_match's filters, since taxon_match is now accessed through taxon_best_match
fix: inputs/.TNRS/schema.sql: MatchedTaxon: use taxon_best_match instead of taxon_match because this should provide only one match per taxon
inputs/.TNRS/schema.sql: added taxon_best_match view
inputs/.TNRS/schema.sql: taxon_match: added taxon_match__one_selected_match unique index
inputs/.TNRS/schema.sql: taxon_match__fill(): split into separate DECLARE blocks for each field for clarity
inputs/.TNRS/data.sql: refreshed
fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*
inputs/.TNRS/schema.sql: taxon_match: insert names via taxon_match_input auto-updatable view instead of directly into taxon_match, to allow the taxon_match columns to be renamed while still supporting inserts using the TNRS column names
inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name
bugfix: inputs/.TNRS/schema.sql: taxon_name_is_safe(): need to use `NOT (_ = ANY()) instead of ` != ANY`, because the != operator is applied to each element
inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables
inputs/.TNRS/schema.sql: `taxon_scrub.scrubbed_unique_taxon_name.*`: added to-modify instructions
inputs/.TNRS/schema.sql: *_modify(): merged these into the "to modify" instructions in the corresponding views, because there is no need to create a separate *_modify() function for every view now that their definitions are all the same
schemas/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "
*: use vegbiendev:/home/bien instead of /home/bien/svn
merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
removed no longer needed inputs/VegBIEN/fs symlink. use web/.fs instead.
inputs/.TNRS/schema.sql: unsafe_taxon_names(): removed the name with "spp." now that this TNRS bug (https://pods.iplantcollaborative.org/jira/browse/TNRS-193) has been fixed
inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()
inputs/.TNRS/schema.sql: added taxon_name_is_safe()
inputs/.TNRS/schema.sql: added unsafe_taxon_names()
bugfix: **/.htaccess: redirects with fragment: qsappend does not support fragment, so append it separately
bugfix: inputs/.TNRS/.htaccess: qsappend does not support fragment, so append it separately
bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields
inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this
lib/tnrs.py: switched to downloading all matches per name, as is needed to implement #917. note that this will break the parts of the schema that use the tnrs table, until Brad's match-picking algorithm can be implemented, but this tradeoff is necessary to be able to begin scrubbing sooner (Martha; wiki.vegpath.org/2014-05-29_conference_call#TNRS)
schemas/vegbien.sql: tnrs_input_name: don't scrub accepted names, as using multiple matches per name no longer provides a single accepted name to scrub. instead, the Accepted_* fields can be whitespace-split to generate the same columns that would have been generated by the scrubbing (and without the overhead of the extra TNRS call).
fix: inputs/.TNRS/schema.sql: added back index on Name_submitted, which is needed for tnrs_input_name to work properly (now that there is no automatic index created by a unique constraint)
fix: inputs/.TNRS/schema.sql: tnrs: removed unique constraint on Name_submitted, Name_matched because there can be more than one match with the same Name_matched (but different accepted names, etc.)
fix: inputs/.TNRS/schema.sql: tnrs.tnrs__valid_match index: made it non-unique to allow multiple matches per name, as is needed to implement #917
bugfix: inputs/.TNRS/schema.sql: tnrs__match_num__fill(): only fill if not set, to support case where tnrs is being restored from a .sql file (where match_num is already set)
inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)
inputs/.TNRS/schema.sql: unique constraint on Name_submitted: added Name_matched to allow multiple matches per name, as is needed to implement #917
inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column
inputs/.TNRS/schema.sql: tnrs: pkey: use match_num instead of Name_number to allow multiple matches per name, as is needed to implement #917
inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated
inputs/.TNRS/schema.sql: tnrs: populate match_num
inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns
inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line
inputs/test_taxonomic_names/_scrub/*: updated to TNRS schema
inputs/.TNRS/schema.sql: tnrs: added match_num
inputs/.TNRS/data.sql.run: refresh(): documented runtime (1 min)
inputs/.TNRS/schema.sql: added tnrs__match_num__next()
inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
inputs/.TNRS/schema.sql: taxon_scrub.scrubbed_unique_taxon_name.*: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*
inputs/.TNRS/schema.sql: taxon_scrub: documented how to modify it
inputs/.TNRS/schema.sql: added taxon_scrub_modify()
inputs/.TNRS/schema.sql: MatchedTaxon_modify(): use simpler util.recreate_view()
inputs/.TNRS/schema.sql: MatchedTaxon_modify(): documented usage
inputs/.TNRS/schema.sql: MatchedTaxon_modify(): removed no longer needed DROP VIEW statement
fix: schemas/util.sql: force_recreate(): renamed to just recreate(), because "force" normally implies that things will be deleted, which this function does not do
fix: inputs/.TNRS/schema.sql: MatchedTaxon.taxonomicStatus: filter using map_taxonomic_status() so that the corrected value is available in the normalized DB, not just analytical_stem
inputs/.TNRS/schema.sql: MatchedTaxon: to modify: use new MatchedTaxon_modify(), which eliminates the work of putting together the dependent views
inputs/.TNRS/schema.sql: added MatchedTaxon_modify()
bugfix: inputs/.TNRS/schema.sql: map_taxonomic_status(): need to use accepted name instead of scrubbed name (which also includes no-opinion names), as described at http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields. this used to be the accepted name, but got switched when the concatenated name was also used to store the matched name for no-opinion names.
inputs/.TNRS/schema.sql: MatchedTaxon: documented how to modify it (using util.force_recreate())
inputs/.TNRS/schema.sql: MatchedTaxon, etc.: added accepted_morphospecies_binomial derived field
inputs/.TNRS/schema.sql: MatchedTaxon.Accepted_name_species: mapped to accepted_species_binomial
fix: inputs/.TNRS/schema.sql: COMMENTs: always include newline before and after
bugfix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: undid rename of accepted name columns to scrubbed_* (r13435), because these are actually not the same (scrubbed_* is the combination of accepted and no-opinion names). the accepted name columns will now be named accepted_*, following the standard naming scheme.
fix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: scrubbed_*: use columns from MatchedTaxon whenever possible, to as much as possible avoid the need to join to taxon_scrub.scrubbed_unique_taxon_name.*
bugfix: inputs/.TNRS/grants.sql: added GRANT statements from schema.sql because these aren't run by `make inputs/.TNRS/reinstall`
bugfix: inputs/input.Makefile: $(datasrc_schema_exists): need to use $(datasrc), not $(schema), as $schema is only what this var is called in the runscripts
bugfix: inputs/analytical_db/: need dummy table.run file to cause a schema to be created for this datasource
fix: inputs/input.Makefile: $(sortFile): don't print the "add any missing tables to $(sortFile)" message every time the Makefile is run
