**/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/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, _license/VegBank_schema/LICENSE.TXT: moved text of the GPL2 license into separate file _license/GPL2.txt to avoid cluttering up LICENSE.TXT

/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/*/: 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

_license/ESA/: renamed to VegBank_schema/ because this license applies only to the VegBank schema

_license/README.TXT: merged ¶2 into ¶1

_license/README.TXT: replaced "authority information proving the open-source status" with the simpler "open-source proof". clarified that each LICENSE.TXT is meant as a proof.

/LICENSE.TXT: added note that when redistributing, it recommended to include _license/, so that the open-source proof is included along with the license text (this information should be here as well as in _license/README.TXT because redistributors might not think to look in that file)

/LICENSE.TXT: removed "svn" before "repository" because this would apply equally to a git export of the repository

/LICENSE.TXT: replaced "portions" with "parts" for consistency with the _license/README.TXT wording

_license/README.TXT: clarified that this folder contains authority information proving the open-source status of parts of the codebase. added recommendation to include this folder when redistributing, so that the open-source proof is included along with the license text.

_license/LICENSE.TXT: renamed to README.TXT because this actually contains a description of the folder, not license text

schemas/Makefile: removed no longer used rename/%, rotate. use %/install, %/publish instead to manage public schema versions.

schemas/Makefile: removed no longer needed public/uninstall, which is handled more generally by `%/uninstall: vegbien.sql` instead

schemas/Makefile: `%/uninstall: vegbien.sql`: added support for *_validation schema

schemas/Makefile: %/uninstall: split into 2 rules like for %/install, so that different actions can easily be added for the public schema

schemas/Makefile: %/publish: support auxiliary *_validation schemas

bugfix: schemas/Makefile: `%/install: vegbien.sql`: need -e before each s/// expression

schemas/Makefile: `%/install: vegbien.sql`: create a custom _validation schema for *each public schema, rather than one for the most recently-created public schema. this allows validations to continue to be run against a previous version of the DB while a new version is being imported.

validation/aggregating/traits/bien3_validations_traits_bien3.sql: include only records from the bien2_traits datasource, to ensure that the scope of all queries is limited to the datasource

validation/aggregating/*/*.sql (the output queries): added `SET search_path TO validation`

validation/aggregating/specimens/qualitative_validations_specimens.sql: added CREATE VIEW prefixes using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW

validation/aggregating/traits/bien3_validations_traits_bien3.sql: added CREATE VIEW prefixes using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW

validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: added CREATE VIEW prefixes using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW

validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: added CREATE VIEW prefixes using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW

added validation/aggregating/specimens/qualitative_validations_specimens.sql template, with query descriptions from NY/qualitative_validations_source_db_NYBG.sql

validation/**: removed old versions of by=-tagged files. these were not renamed in the last commit because there were newer versions that they collided with. note that because , sorts before . , the newer version (with more ",name@inst" tags) was correctly renamed instead of the older version.

validation/**: removed by=... indicators so that we don't have to add an author name every time a file is changed. the author indicator is not needed now that both Brad's and my edits are open-source.

inputs/bien2_traits/TraitObservation/postprocess.sql: remove rows with no taxon name, which are invalid, and which helps simplify the aggregating validations queries

added validation/aggregating/pipeline/aggregating_validations_pipeline.odg with .png export

added validation/aggregating/plots/FIA/bien3_validations_fia_input.sql.eml.txt. note that a .url file is not needed because this information is in the .eml.txt file.

fix: validation/aggregating/traits/_archive/bien3_validations_traits_bien3.by=Brad@iPlant.sql: renamed to indicate that this is actually not Brad's original file, as the filename would seem to indicate

added validation/aggregating/plots/FIA/

validation/aggregating/*.by=Brad@iPlant*: placed under version control, since these are now open-source

validation/**: removed svn:ignore exclusion of iPlant-owned files, since these are now open-source

fix: inputs/VegBIEN/Redmine/svn/.htaccess: updated repository URL to point to trunk/

added wiki/LICENSE.TXT,_license/, with license terms that apply specifically to the wiki (which is BSD, not GPL). note that the wiki attachments are NOT open-source, only the page text.

schemas/vegbien.ERD.mwb: regenerated exports

_license/VegBank/: renamed to ESA/ following the convention that each _license/ subfolder is a copyright owner

/LICENSE.TXT: added collective license conditions (GPL2+) for the svn repository as a whole, except the non-open-source portions

added _license/VegBank/

added LICENSE.TXT and related files (in _license/). the open-source portions of the svn repository are licensed as described in _license/. note that some portions of the svn repository are NOT open-source. these are copyright their respective owners.

schemas/vegbien.ERD.mwb: synced to schemas/vegbien.my.sql, which adds the validation schema

schemas/util.sql: added diff_views()

schemas/util.sql: added diff_cols(), for use with the aggregating validations

bugfix: schemas/Makefile: public/uninstall: need to uninstall the validation schema in addition to the public schema (deleting the public schema would only cascade to the contents of the validation schema)

schemas/vegbien.sql: added validation schema, which contains queries used in the aggregating validations. schemas/Makefile: include schemas that depend on `public` (eg. `validation`) so they are restored along with it.

bugfix: bin/pg_dump_vegbien: fixed arg-count check to allow passing command-line options to pg_dump via args

bugfix: inputs/SALVIAS/verify/plots.out.sql: fixed ' quoting syntax to use '' instead of \' to escape '

inputs/input.Makefile: verify/%.out: use a *.sql file in the verify/ directory itself to generate *.out, so that each datasource can have its own set of output queries. for datasources that should share the same set of queries, they can instead be symlinked to the same file.

fix: inputs/CVS/project/: added _no_import since this should not also be imported separately from taxon_observation.**

fix: validation/aggregating/traits/_archive/bien3_validations_traits_bien3.by=Brad@iPlant,Aaron@UCSB,Brad@iPlant.sql: added missing .url extension

added validation/aggregating/traits/_archive/bien3_validations_traits_bien3.by=Brad@iPlant,Aaron@UCSB,Brad@iPlant.sql

validation/aggregating/traits/BIEN2_traits/_archive/bien3_validations_traits_original_mysql.by=Brad@iPlant,Aaron@UCSB,Brad@iPlant.sql.url: renamed to indicate that it's just by Brad (it was the other file, the output queries, that were created by both of us)

added validation/aggregating/traits/BIEN2_traits/_archive/bien3_validations_traits_original_mysql.by=Brad@iPlant,Aaron@UCSB,Brad@iPlant.sql.url

validation/aggregating/plots/_archive/bien3_validations_salvias_vegbien.by=Brad@iPlant.sql.url: removed trailing @

deleted validation/aggregating/traits/_archive/bien3_validations_traits_bien3.by=Brad@iPlant.sql.url@, since there is already a version without the trailing @

validation/aggregating/traits/BIEN2_traits/_archive/bien3_validations_traits_original.by=Brad@iPlant.sql.url: removed trailing (apparently, the escape for paths containing @ should only be used on the input path)

added inputs/XAL/Specimen/_no_import, since this is a demo-only datasource and there isn't a staging table for it

inputs/.geoscrub/county_centroids/test.xml.ref, inputs/.NCBI/{names.src,nodes.src}/test.xml.ref: accepted test outputs (generated now that these tables are in import_order.txt)

inputs/FIA/taxon_observation.**/header.csv: updated for new REF_RESEARCH_STATION.country metadata value col

/README.TXT: Full database import: `make test by_col=1`: documented runtime (20 min)

/README.TXT: Full database import: `. bin/import_all`: documented how to view progress

fix: schemas/Makefile: %/uninstall: don't prompt to delete auxiliary schemas, as these do not contain data