schemas/util.sql: diff_cols(): embed left_query/right_query directly in the main SQL statement, so that the query planner can take the sort order of the queries into account in planning the FULL JOIN (and where possible, use a fast merge join)
schemas/vegbien.sql: regenerated from DB, which adds an autogenerated column alias
schemas/vegbien.sql, validation/aggregating/*/*.sql: renamed public_validation_* to plural public_validations_* since we refer to them as aggregating validation*s*
schemas/util.sql: added eval2col_pair()
web/.phpPgAdmin/.htaccess: support linking to a function
web/.phpPgAdmin/.htaccess: support linking to the functions list
web/.phpPgAdmin/.htaccess: support linking to a view
web/.phpPgAdmin/.htaccess: allow linking directly to the views list of a schema
added backups/vegbien.r12025.backup.md5
web/.phpPgAdmin/.htaccess: refactored to build the URL incrementally, extracting path components 1st->last, instead of handling each # of path components as a separate case (which was more rigid and created unnecessary duplication)
backups/TNRS.backup.md5: updated
bugfix: web/.phpPgAdmin/.htaccess: path RewriteRules: need to go directly to the applicable tab, rather than going via redirect.php, because redirect.php will use the last selected tab, rather than the first tab for that section, leading to unexpected results when a non-default tab was previously selected
validation/aggregating/pipeline/aggregating_validations_pipeline.odg: made "diff tables" the same size as the other major labels
validation/aggregating/pipeline/aggregating_validations_pipeline.odg: added CSVs export arrows and import process arrows, as decided in conference call
schemas/vegbien.sql: public_validation_plots: added Brad's notes as comments
schemas/vegbien.sql: public_validation_plots: populated queries from validation/aggregating/plots/bien3_validations_salvias_vegbien.sql
validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: _12_count_of_verbatim_taxa_per_plot_in_each_project: removed typo (in the original queries, not added by the refactoring)
validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: shortened view names to fit in the 63-char limit
schemas/vegbien.sql: public_validation_traits: added Brad's notes as comments
schemas/vegbien.sql: public_validation_traits: populated queries from validation/aggregating/traits/bien3_validations_traits_bien3.sql
validation/aggregating/*/*.sql: use "" to preserve case in column aliases, so that they match the input queries
validation/aggregating/*/*.sql: use current_schema instead of a hardcoded datasource name or psql variable
validation/aggregating/*/*.sql: search_path: added public
validation/aggregating/*/*.sql: use the new type-specific validation schema names
validation/aggregating/*/*.sql: removed type-specific prefix from the view name, which is now part of the validation schema
inputs/import.stats.xls: updated import times
schemas/vegbien.sql: analytical_stem.datasource: removed fkey to source.shortname because this prevents individually-reloaded datasources from being published
schemas/vegbien.sql: publish(), rm(): documented runtime (1 min)
schemas/vegbien.sql: added datasource_unpublish()
lib/sql_io.py: automatic handling of input/output column type mismatches: also do this for identifying columns, which first cause an error in a join in sql.distinct_table() rather than in the main insert (and thus were not handled by the existing error handling). previously, the user would have had to manually cast the input column in postprocess.sql. this involves getting handle_MissingCastException() to update join_cols as well as mapping.
lib/sql.py: distinct_table(): don't cache the table creation, because this prevents different distinct_tables from being created for the same input table
lib/sql.py: create_table(), copy_table_struct(): support custom query options, such as cacheable
lib/sql_io.py: put_table(): main loop MissingCastException handler: factored out into nested function so that it can also be used elsewhere
lib/sql.py: parse_exception(): parse "operator does not exist" errors as MissingCastExceptions (these appear when a staging table column is of the wrong type)
bugfix: /README.TXT: Full database import: Check that source contains [# datasources] rows up through XAL: added alternative verification method when this is not the case (some datasources may be near the end depending on import order)
schemas/vegbien.sql: public_validation: split into separate subschemas for plots, specimens, traits
schemas/Makefile: vegbien.sql: support auxiliary schemas besides *_validation
fix: schemas/Makefile: %/publish: removed no longer applicable instructions about running `make schemas/rotate`. you should not publish a schema until you are satisfied that it can replace the previous public schema, so that the previous public schema doesn't need to be saved.
fix: schemas/vegbien.sql: public_validation comment: undid incorrect replacement of "validation" with "public_validation"
bugfix: schemas/Makefile: "public": dont
schemas/Makefile: %/publish: don't ignore errors if schema doesn't exist, because it should always exist if you are publishing it
schemas/Makefile: `%/uninstall: vegbien.sql`: use util.schema_bundle_rm() instead of public.rm(), because when the public schema is incompletely imported, public.rm() will not yet exist
schemas/Makefile: `%/install: vegbien.sql`: support auxiliary schemas besides *_validation
schemas/Makefile: %/uninstall, %/publish: use new public.rm(), publish(), which encapsulate the process of renaming multiple related schemas and also allow additional auxiliary schemas beyond just *_validation
schemas/vegbien.sql: added rm(), which deletes this schema
schemas/vegbien.sql: added publish(), which publishes this schema
schemas/vegbien.sql: added public_schema_publish()
schemas/util.sql: added functions for maintaining schema bundles, groups of schemas with a common prefix
schemas/util.sql: added schema_bundle_get_schemas()
schemas/util.sql: added schema_replace()
schemas/util.sql: added schema_rm(), schema_rename()
schemas/vegbien.sql: datasource_publish(): removed nested transaction, which is not needed because Postgres runs each top-level command in a transaction (including in autocommit mode)
bugfix: schemas/Makefile,vegbien.sql: renamed validation to public_validation to match the suffixed name applied by `make schemas/public/install`
schemas/Makefile: %/install, %/publish for public schema: added usage
/README.TXT: to back up the version history: added back `git svn fetch` so we keep the git export up-to-date, too
/README.TXT: to back up the version history: added runtimes (1.5 h for the initial svnsync)
/README.TXT: to back up the version history: added trailing /s to dirs
bugfix: /README.TXT: to back up the version history: fixed svn_repo/ path
**/LICENSE.TXT: corrected "it recommended" to "it is recommended"
_license/non-open-source/applies_to.txt: deleted items: tip revision needs to refer to the revision at which the problem was discovered, not the revision before that
_license/non-open-source/applies_to.txt: deleted items: clarified that some things deleted after r11705 (when we started copyright scrubbing) might also be non-open-source, because they might have been deleted for reasons other than copyright scrubbing and thus would be missing the "copyright scrub" tag
/LICENSE.TXT: removed separate non-open-source disclaimer about parts of the version history before r11705, because this is now listed in _license/non-open-source/applies_to.txt
_license/non-open-source/applies_to.txt: included deleted items that are non-open-source, so that the list correctly applies to the entire repository (which includes the version history)
**/LICENSE.TXT: disclaimer about things that are not open-source: removed "these are copyright their respective owners", because this is understood
_license/README.TXT: changed "parts" to "components" for clarity
_license/non-open-source/applies_to.txt: UArizona?: added BIEN2/traits_observation_counts.xls
/README.TXT: to back up the version history: use svnsync instead of `git svn fetch`, so that the backup is in a format that can be directly reimported into an svn repo
/LICENSE.TXT: parts of the repository that are not open-source: added ,s to clarify the meaning
/LICENSE.TXT: documented that this license refers specifically to the repository hosted at https://code.nceas.ucsb.edu/code/projects/bien/trunk/, since we also have a publicly-accessible checkout at http://fs.vegpath.org/, which contains numerous non-open-source files (more than are listed in _license/non-open-source/applies_to.txt)
fix: inputs/VegBIEN/Redmine/wiki/.htaccess: redirect to new main page when accessed without trailing /
web/BIEN3: redirected to .wiki since the wiki homepage now contains the list of all BIEN3 components
web/links/index.htm: updated to Firefox bookmarks. Quick links: use bien3.vegpath.org to link to the main BIEN3 page
added web/BIEN3 symlink, with .bien3 case-insensitive alias
_license/*/applies_to.txt: added exclusion for "UCSB modifications"
added _license/GPL2.txt.url
/LICENSE.TXT, _license/VegBank_schema/LICENSE.TXT: moved text of the GPL2 license into separate file _license/GPL2.txt to avoid cluttering up LICENSE.TXT
_license/*/LICENSE.TXT: documented that the first section of the file is from license.eml.txt in each folder
/LICENSE.TXT: GPL text: include the full range of copyright years
/LICENSE.TXT: added disclaimer that parts of the version history before r11705 (2013-11-21) are NOT open-source. this is the revision of the first copyright scrub.
added issues/ with LICENSE.TXT for the issue tracker (BSD)
wiki/_license/*/: symlink the contents instead of the folders, because the root dir's and wiki's applies_to.txt's will be different
wiki/LICENSE.TXT: documented what this license refers to (the wiki hosted at https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/)
wiki/LICENSE.TXT: added message about including _license/ when redistributing, as for /LICENSE.TXT
wiki/_license/LICENSE.TXT: replaced with README.TXT as in /_license
wiki/LICENSE.TXT: changed "the page text of the wiki" to "the wiki's components" since some of the attachments will eventually be marked as open-source
/LICENSE.TXT: moved emphasized sections to top
/LICENSE.TXT: changed "the open-source parts of the repository" to "the repository's components" so that this sentence makes sense once the non-open-source exception is removed
/LICENSE.TXT: documented that the non-open-source files are now listed in _license/non-open-source/applies_to.txt
added _license/non-open-source/applies_to.txt
removed schemas/VegX/run.py, which is a duplicate of _archive/bienDjango/trunk/bien/v/models.py (this may have ended up here because it was a wiki page attachment, but the initial revision did not indicate the source)
added _license/VegBank_schema/applies_to.txt
schemas/VegCore/vegbien_identifier_examples.xlsx: changed to symlink to Brad_Boyle/vegbien_identifier_examples.xlsx, to avoid duplicate copies
added _license/TWiki/ (for inputs/VegBIEN/TWiki/)
added _license/PostgreSQL_config (for schemas/*.conf)
*/LICENSE.TXT: GPL: removed divider between the copyright header and license text, since these are part of the same license
