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
_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
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)
(apparently, the
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
schemas/vegbien.sql: added top_plot view
/README.TXT: to back up the version history: added steps to sync the git repository to jupiter and the local machine
/README.TXT: added steps to back up the version history
validation/aggregating/plots/bien3_validations_salvias_vegbien.by=Brad@iPlant.sql.url: moved to _archive/ so only the most recent version would be in the main plots/ directory
planning/resources/dev_machine.specs/sys_info.spx+/system_power_settings.txt: updated: enabled "Automatic Restart on Power Loss" and "Wake on LAN" for UPS (this requires using pmset, as described at http://vegpath.org/links/#pmset%281%29%20Mac%20OS%20X%20Manual%20Page )
web/links/index.htm: updated to Firefox bookmarks: wake for network access: added link to pmset man page, which contains commands for setting "wake for network access" for all power sources. note that "automatic restart on power loss" also needs to be set for all power sources, because the computer will always be in UPS mode at the time of a power failure.
inputs/input.Makefile: add!: verify/: also svn:ignore *.tsv, *.txt
validation/aggregating/traits/bien3_validations_traits_bien3.by=Brad@iPlant.sql*: moved to _archive/
validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original.by=Brad@iPlant.sql*: moved to _archive/
schemas/vegbien.sql: location_set_top_plot(): only do the lookup of the parent's top_plot when there is a parent_id
schemas/vegbien.sql: location: added autopopulated top_plot
schemas/vegbien.sql: locationevent: added locationevent_pull_forward_from_parent() trigger which populates project_id from the parent locationevent
web/links/index.htm: updated to Firefox bookmarks: NCEAS: added link to phone list, which contains the Balboa Building maintenance numbers
/README.TXT: Notes on running programs: added warning that you should always start with a clean shell to avoid spurious bugs
