*: 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/publishable datasources.xlsx: updated
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
bugfix: inputs/input.Makefile: install: only run this for datasource dirs
inputs/input.Makefile: install: use ./run's install target for clarity
bugfix: inputs/input.Makefile: install: made it idempotent (using new $(datasrc_schema_exists)) so that it could be run by `make install` on an existing system
bugfix: inputs/input.Makefile: $(datasrc_schema_exists): need to use $(shell ...)
inputs/input.Makefile: added $(datasrc_schema_exists)
added inputs/VegBank/verify/outputBien.log.url
inputs/input.Makefile: add: verify/: also svn:ignore *.log
bugfix: inputs/input.Makefile: %/postprocess: invoke runscript if it exists
lib/runscripts/validations.pg.sql.run: export_(): make the export idempotent for easier re-runnability
fix: lib/runscripts/file.pg.sql.run: removed include of in_datasrc_dir.run, because this location does not apply to all .sql export scripts
bugfix: inputs/input.Makefile: validations.sql must be in a subdir so it won't get run by sql/install
inputs/input.Makefile: install: also run validate/install
inputs/input.Makefile: added validate/install
bugfix: inputs/SALVIAS/validations.sql: need to cast character varying to text so that the types of each side of if() match
bugfix: **/postprocess.sql: don't use the public schema, because this creates an unsatisfied dependency while the database is being installed, and breaks `make install`
inputs/GBIF/_MySQL/.rsync_ignore: added GBIFPortalDB-*.data.sql.gz, because these are intermediate files
inputs/Madidi/_src/: set svn:ignore
fix: inputs/SALVIAS/projects/postprocess.sql: remove private data that should not be publicly visible: preserve datasets with ipr_specific = '', because they are actually redistributable, according to Brad (http://wiki.vegpath.org/2014-04-17_conference_call#conditions-of-use)
bugfix: inputs/NY/validations.sql: _specimens_07_list_of_verbatim_subspecific_taxa_with_author: updated filter condition to match output query
inputs/NY/run: `make inputs/NY/validate`: updated runtime (8 min, with added queries)
fix: inputs/NY/Ecatalog_all/map.csv, postprocess.sql: remapped substrate, vegetation to locationRemarks
bugfix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13*: also need to include coordinate pairs which have one of their coordinates NULL, by using OR instead of AND
bugfix: inputs/NY/validations.sql: _specimens_13b_list_of_all_decimal_lat_long: matched column types to output query
bugfix: inputs/NY/validations.sql: _specimens_13a_list_of_all_verbatim_lat_long: matched column types to output query
inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: added breakdowns _specimens_13a_list_of_all_verbatim_lat_long, _specimens_13b_list_of_all_decimal_lat_long to help troubleshoot the diff
fix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: count lat/longs together instead of separately, because the DISTINCT is by coordinate pair, not individual coordinate value (which wouldn't make much sense)
fix: inputs/NY/validations.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: use new is_castable(), which is much more accurate than Brad's custom regexp for determining if something is numeric
inputs/NY/validations.-.util.sql: added util.is_castable() wrapper
bugfix: inputs/NY/validations.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: need to include both lat and long in the value to DISTINCT on
fix: inputs/NY/validations.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: need to DISTINCT the values that are being counted, because they are merged by the coordinates_unique unique constraint in the import
inputs/NY/run: `make inputs/NY/validate`: documented slow queries: _specimens_12_distinct_collector_name_collect_num_date_w_count
inputs/SALVIAS/run_: `make inputs/SALVIAS/validate`: documented slow queries (_plots_06a_list_of_stems). these may need to have their query plans rechecked.
inputs/NY/run, inputs/SALVIAS/run_: `make inputs/.../validate`: updated runtime (+2 min)
fix: inputs/NY/validations.sql: specimens*_of_unique_verbatim_author_taxa_with_genus: use scientificName rather than the concatenated ranks, because that is what is imported to taxonlabel.taxonomicname
mappings/VegCore-VegBIEN.csv: mapped subspecies to new taxonverbatim.subspecies for easier access by validations queries
fix: inputs/test_taxonomic_names/Taxon/map.csv: scientificName: remapped to scientificName instead of taxonName as this does include the author for some names
fix: inputs/NY/Ecatalog_all/map.csv: ScientificName: remapped to scientificName instead of taxonName as this does include the author
fix: inputs/NY/validations.sql: specimens*_of_unique_verb_subsp_taxa_with_author: use taxonName instead of concatenating the ranks, as that corresponds to what we use as the concatenated taxonomic name
