schemas/util.sql: added ~ operator for ranges

schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: allow geovalid_bien = NULL to enable filtering New World status by coordinates rather than country

schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: added geovalid_bien

schemas/VegCore/.htaccess: RewriteBase: use full path

schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/

schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/

added schemas/VegBIEN/data_dictionary/create_bien3_viewFullOccurrence.txt from Brad

schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/

added schemas/VegBIEN/data_dictionary/schema_docum.pptx from Brian McGill

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

schemas/VegBIEN/VegBIEN data dictionary.xlsx: moved to schemas/VegBIEN/data_dictionary/

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: analytical_stem_view: approved by/to discuss: renamed to * (removing "approved by") because the participants in today's conference call indicated that they were happy with the definitions, and the issues raised before the call had been addressed

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added all tables used to create analytical_stem_view, not just those that Brian M listed. (Brian M generated his tables list from the analytical_stem_view columns rather than the joins, and renamed plot.** to plot, which is why his list ended up missing tables and in the wrong order.)

schemas/vegbien.sql: added 2014-6-12.Jeff_Ott.climatic_range_determinants (wiki.vegpath.org/Data_requests)

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: resized columns to fit laptop screen

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added my and Brian McGill's notes from the data dictionary conference call

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added analytical_stem_view table definitions

removed schemas/vegbien.ERD.MySQL_Workbench_6.1.6.mwb, because vegbien.ERD.mwb is now targeted to the correct version of MySQL Workbench (and is more up-to-date)

schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added "to discuss" column requested by Martha. resized columns to avoid truncating the viewFullOccurrence term names.

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating definitions of terms

added schemas/DwC/hist symlink to history/ to help fit URLs in the 63-char limit

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating viewFullOccurrence->analytical_stem_view and analytical_stem_view->viewFullOccurrence mappings

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: use new deletion comments (with () ) to indicate portions of external terms whose semantic meaning does not apply to our usage

web/username_prefix.php: comments: use [] instead of () because in writing, [] denotes insertion, while () (as an editing mark) denotes something to remove

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: removed extra rows and columns so that they aren't included when copying and pasting

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added tab to store viewFullOccurrence->analytical_stem_view mapping

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added viewFullOccurrence column

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added links to editable and clickable versions of the spreadsheet, to enable switching back and forth between them. populated more definitions and links.

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: populated some definitions from VegCore data dictionary where available

bugfix: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: restored "" that had been stripped out when the data was copied out and pasted back, due to a bug in Google spreadsheets. prepended : before initial " as a workaround to prevent the " getting stripped out again.

schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated

schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database

fix: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: restored "" that had been stripped out when the data was pasted in. set column widths to fit on a laptop screen.

added schemas/VegBIEN/VegBIEN data dictionary.xlsx

schemas/public_.sql: analytical_stem_view: example terms from each source: added location in the VegBIEN core DB

schemas/public_.sql: analytical_stem_view: terms in normalized schemas: put the source name right next to the term name (instead of after the table name) so it's easy to find

schemas/public_.sql: analytical_stem_view: VegX terms: populated definitions

schemas/public_.sql: analytical_stem_view: VegX terms: referenced to the specific table/subpath that they are in

bugfix: schemas/public_.sql: analytical_stem_view: locationName: re-sourced to VegX because this is actually not a DwC term

schemas/public_.sql: analytical_stem_view: populated definitions of linked DwC terms from DwC data dictionary

schemas/public_.sql: analytical_stem_view: renamed terms to link URLs, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#data-dictionary-rename-terms-to-link-URLs

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

schemas/public_.sql: analytical_stem_view: populated links from unrenamed term names, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#data-dictionary-populate-links-from-unrenamed-term-names

fix: schemas/public_.sql: analytical_stem_view: links: removed = before them because the link is in fact one member in a list of definitions (the = would apply to all definitions, not just the link, and since it apply to all definitions, it's redundant because of course the comment is what the column equals)

fix: schemas/public_.sql: analytical_stem_view: vegpath.org links: use ; instead of : between link and definition, because it makes more grammatical sense

schemas/public_.sql: analytical_stem_view: vegpath.org links: removed no longer needed // suffix

schemas/public_.sql: analytical_stem_view: added links and definitions for half a dozen of the terms from various sources

schemas/public_.sql: analytical_stem_view: indicated provenance of the rest of the terms

schemas/public_.sql: analytical_stem_view: flagged the DwC terms

schemas/public_.sql: added plot.**.modify()

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: *_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()

fix: schemas/util.sql: view_def_to_orig(): also need to merge .* expressions resulting from a SELECT * of a join, to avoid duplicated columns

fix: schemas/util.sql: view_def_to_orig(): require at least 6 cols to avoid false positives in the expansion match pattern

bugfix: schemas/util.sql: view_def_to_orig(): 1st col: can't prepend \y because it considers only \w chars, not "

bugfix: schemas/util.sql: view_def_to_orig(): don't match whitespace in the middle of a "" identifier, as this could throw off the parser

schemas/util.sql: eval(): restore user's intent by running util.view_def_to_orig() on the query to unexpand expanded * expressions

schemas/util.sql: pg_get_viewdef(): use util.view_def_to_orig()

schemas/util.sql: added view_def_to_orig()

fix: schemas/util.sql: pg_get_viewdef(): should be STABLE because it references system catalogs

schemas/util.sql: added pg_get_viewdef() wrapper, which unexpands expanded * expressions

fix: schemas/public_.sql: tnrs_input_name: added ORDER BY to ensure a stable sort order. this also creates better query plans by enabling merge joins.

bugfix: schemas/public_.sql: tnrs_input_name: need to exclude unsafe taxon names as a workaround to #935 (TNRS crashes when scrubbing names with two infraspecific epithets)

schemas/public_.sql: taxonlabel: added index on taxonomicname to facilitate retrieving rows from tnrs_input_name

inputs/.TNRS/schema.sql: added taxon_name_is_safe()

inputs/.TNRS/schema.sql: added unsafe_taxon_names()

schemas/public_.sql: sync_*(): renamed to *_modify() to facilitate finding these functions when modifying the corresponding view (using the new naming convention for a view's on-modify function)

bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields

bugfix: schemas/util.sql: mk_drop_from_create(): need to match first rather than last CREATE

inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this

schemas/util.sql: recreate_view(): support omitting the view_query if the view has already been modified (eg. for public.*_view, which allow changing the view as a separate step)

fix: schemas/public_.sql: sync_*(): use util.copy() instead of CREATE TABLE AS so that table and column comments are also copied. this avoids the need to separately add the same comments to the view and its materialized table.

bugfix: schemas/util.sql: recreate(): need to handle case where util.mk_drop_from_create() is NULL

bugfix: schemas/util.sql: mk_drop_from_create(): only match CREATE if no custom DROP came before it

bugfix: schemas/public_.sql: sync_geoscrub_input_to_view(): `CREATE TABLE geoscrub_input AS __`: needs `LIMIT 0`

fix: schemas/util.sql: explain2notice_msg_if_can(): also need to catch invalid_cursor_definition ("cannot open multi-query plan as cursor")

schemas/public_.sql: sync_analytical_stem_to_view(): removed DROP TABLE IF EXISTS because this is now done automatically by util.recreate()

schemas/util.sql: added copy()

schemas/util.sql: added copy_data()

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)

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: 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/.TNRS/schema.sql: tnrs: added match_num

schemas/Makefile: added back rename/%, which is used by `inputs/.TNRS/data.sql.run refresh`. updated it to use schema bundles.

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)

schemas/util.sql: added seq__reset()