Activity
From 01/16/2014 to 02/14/2014
02/14/2014
- 04:36 PM Revision 12225: _license/non-open-source/applies_to.txt: clarified that this is an exclusions list, not an inclusions list, in terms of what's open-source
- 03:09 PM Revision 12224: validation/aggregating/*/*.sql, schemas/vegbien.sql, lib/runscripts/validations.pg.sql.run, inputs/bien2_traits/validations.sql: added _ to beginning of each view name so the validation views would sort at the top in the datasource's tables list. this will also make the validation result sets easily distinguishable from the data tables.
- 02:34 PM Revision 12223: validation/aggregating/*/*.sql: renamed views to match the current naming scheme in the DB. these files still need to be kept up-to-date because there are some queries that haven't been implemented yet, and therefore exist only in these files, not the DB.
- 12:39 PM Revision 12222: schemas/util.sql: ifnull(): use COALESCE() instead, because it turns out that MySQL's IFNULL() is just a special case of this
- 12:20 PM Revision 12221: added inputs/bien2_traits/validations.sql, from validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original_mysql.VegCore.sql
- 12:20 PM Revision 12220: inputs/input.Makefile: $(svnFilesGlob): added validations.sql
- 12:03 PM Revision 12219: bugfix: validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original_mysql.VegCore.sql: added util to search_path so that IFNULL() would link to util.ifnull()
- 11:55 AM Revision 12218: schemas/util.sql: added ifnull(), equivalent to MySQL's IFNULL() (Postgres auto-lowercases the name)
- 11:40 AM Revision 12217: lib/sh/util.sh: stderr_matches(): documented that the purpose of not redirecting fd 2 back to fd 2 is to allow log-filtering out an otherwise-confusing benign error
- 11:30 AM Revision 12216: lib/sh/util.sh: ignore_err_msg(): documented that unlike `|| true`, this suppresses only errors caused by a particular error *message*, rather than all error exit statuses
- 11:28 AM Revision 12215: bugfix: lib/runscripts/validations.pg.sql.run: updated table match pattern to include the type prefix that validations queries now contain
- 11:16 AM Revision 12214: bugfix: lib/runscripts/validations.pg.sql.run: --table: need to include explicit schema so that matching tables from other schemas are not included
- 11:00 AM Revision 12213: added inputs/bien2_traits/validations.sql.run
- 11:00 AM Revision 12212: added lib/runscripts/validations.pg.sql.run
- 10:59 AM Revision 12211: lib/sh/util.sh: stdout_contains(): usage: documented that this requires a `{ ... } 41>&1` wrapper
- 10:57 AM Revision 12210: lib/sh/util.sh: stderr2stdout(): clarified that fd 2 is *not* redirected back to fd 2
- 10:55 AM Revision 12209: bugfix: lib/sh/util.sh: stderr_matches(): need to avoid redirecting stderr and stdout to the same place, because this prevents redirecting stdout back to the original stdout after stderr has been filtered using |
- 10:23 AM Revision 12208: lib/sh/util.sh: local_export_array: renamed to just export_array because this was a replacement for export, not local_export
- 10:21 AM Revision 12207: lib/sh/util.sh: local_*array: don't need -a because that it's an array is autodetected by the ()
- 10:20 AM Revision 12206: lib/sh/util.sh: stderr_matches(): actually don't need to declare PIPESTATUS_ in a separate command, because local does support arrays
- 10:18 AM Revision 12205: lib/sh/util.sh: added local_export_array
- 10:17 AM Revision 12204: fix: lib/sh/util.sh: local_array: clarified that this is only needed for older versions of bash (the lack of support for arrays has apparently been fixed)
- 10:12 AM Revision 12203: lib/sh/util.sh: added local_array
- 10:07 AM Revision 12202: fix: lib/sh/util.sh: stderr_matches(): usage: documented that now need to manually rethrow any command error, if applicable
- 10:04 AM Revision 12201: *{.sh,run}: stderr_matches calls: don't need to wrap the command in `"try"` because stderr_matches now does this
- 09:55 AM Revision 12200: fix: lib/sh/util.sh: `shopt -s lastpipe`: suppress error message if not supported
- 09:50 AM Revision 12199: lib/sh/util.sh: ignore_err_msg(): use new stderr_matches alias, which includes prep_try (requires loading new aliases)
- 09:49 AM Revision 12198: bugfix: lib/sh/util.sh: stderr_matches(): need to save PIPESTATUS and then use the saved var because it's reset after each cmd
- 09:39 AM Revision 12197: lib/sh/util.sh: stderr_matches(): place exit status of cmd in $e for use with exception handling
- 09:21 AM Revision 12196: lib/sh/util.sh: set `shopt -s lastpipe`, to allow setting vars in the last command of a pipeline
- 08:43 AM Revision 12195: bugfix: lib/sh/util.sh: ignore_err_msg(): use `try` properly with prep_try and `"try"`
- 08:39 AM Revision 12194: lib/sh/util.sh: added prep_try and use it in try alias. try: documented how to run it with a wrapper command.
- 08:21 AM Revision 12193: lib/sh/db.sh: pg_dump(): ignore "No matching tables were found" error, using new ignore_err_msg()
- 08:20 AM Revision 12192: lib/sh/util.sh: added ignore_err_msg()
- 07:34 AM Revision 12191: lib/sh/db.sh: pg_schema_exists(): documented that `try` is used to suppress the error exit status
- 07:31 AM Revision 12190: lib/sh/util.sh: stderr_matches(): usage: surrounded command in if statement to indicate what context it would usually be used in
02/13/2014
- 05:01 PM Revision 12189: lib/runscripts/file.pg.sql.run, schema.pg.sql.run: support custom options to pg_dump in $@
- 04:10 PM Revision 12188: validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original_mysql.VegCore.sql: added view names using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW
- 04:10 PM Revision 12187: validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original_mysql.VegCore.sql: removed trailing whitespace
- 04:06 PM Revision 12186: schemas/vegbien.sql: public_validations_*: merged into single public_validations schema, with type-specific prefixes for each query, so that datasources can use validations queries from multiple type categories, and so that each datasource doesn't have to indicate which validations output schema it's using
- 02:23 PM Revision 12185: schemas/util.sql: diff_cols(): documented how to run EXPLAIN on the FULL JOIN query
- 02:14 PM Revision 12184: 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)
- 02:09 PM Revision 12183: schemas/vegbien.sql: regenerated from DB, which adds an autogenerated column alias
- 02:06 PM Revision 12182: schemas/vegbien.sql, validation/aggregating/*/*.sql: renamed public_validation_* to plural public_validations_* since we refer to them as aggregating validation*s*
- 02:05 PM Revision 12181: schemas/util.sql: added eval2col_pair()
- 01:23 PM Revision 12180: web/.phpPgAdmin/.htaccess: support linking to a function
- 01:08 PM Revision 12179: web/.phpPgAdmin/.htaccess: support linking to the functions list
- 01:05 PM Revision 12178: web/.phpPgAdmin/.htaccess: support linking to a view
- 12:58 PM Revision 12177: web/.phpPgAdmin/.htaccess: allow linking directly to the views list of a schema
- 12:54 PM Revision 12176: added backups/vegbien.r12025.backup.md5
- 12:54 PM Revision 12175: 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)
- 12:53 PM Revision 12174: backups/TNRS.backup.md5: updated
- 11:47 AM Revision 12173: 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
- 10:41 AM Revision 12172: schemas/vegbien.sql, validation/aggregating/*/*.sql: renamed public_validation_* to plural public_validations_* since we refer to them as aggregating validation*s*
- 10:33 AM Revision 12171: validation/aggregating/pipeline/aggregating_validations_pipeline.odg: made "diff tables" the same size as the other major labels
- 10:30 AM Revision 12170: validation/aggregating/pipeline/aggregating_validations_pipeline.odg: added CSVs export arrows and import process arrows, as decided in conference call
- 08:34 AM Revision 12169: schemas/vegbien.sql: public_validation_plots: added Brad's notes as comments
- 08:29 AM Revision 12168: schemas/vegbien.sql: public_validation_plots: populated queries from validation/aggregating/plots/bien3_validations_salvias_vegbien.sql
- 08:26 AM Revision 12167: 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)
- 08:23 AM Revision 12166: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: shortened view names to fit in the 63-char limit
- 08:20 AM Revision 12165: schemas/vegbien.sql: public_validation_traits: added Brad's notes as comments
- 08:17 AM Revision 12164: schemas/vegbien.sql: public_validation_traits: populated queries from validation/aggregating/traits/bien3_validations_traits_bien3.sql
- 08:02 AM Revision 12163: validation/aggregating/*/*.sql: use "" to preserve case in column aliases, so that they match the input queries
- 07:58 AM Revision 12162: validation/aggregating/*/*.sql: use current_schema instead of a hardcoded datasource name or psql variable
- 07:49 AM Revision 12161: validation/aggregating/*/*.sql: search_path: added public
- 07:45 AM Revision 12160: validation/aggregating/*/*.sql: use the new type-specific validation schema names
- 07:41 AM Revision 12159: validation/aggregating/*/*.sql: removed type-specific prefix from the view name, which is now part of the validation schema
- 07:26 AM Revision 12158: inputs/import.stats.xls: updated import times
- 06:53 AM Revision 12157: inputs/import.stats.xls: updated import times
- 05:58 AM Revision 12156: schemas/vegbien.sql: analytical_stem.datasource: removed fkey to source.shortname because this prevents individually-reloaded datasources from being published
- 05:56 AM Revision 12155: schemas/vegbien.sql: publish(), rm(): documented runtime (1 min)
- 05:49 AM Revision 12154: schemas/vegbien.sql: added datasource_unpublish()
- 03:48 AM Revision 12153: 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.
- 03:37 AM Revision 12152: 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
- 03:36 AM Revision 12151: lib/sql.py: create_table(), copy_table_struct(): support custom query options, such as cacheable
- 12:29 AM Revision 12150: lib/sql_io.py: put_table(): main loop MissingCastException handler: factored out into nested function so that it can also be used elsewhere
- 12:01 AM Revision 12149: 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)
02/08/2014
- 11:17 PM Revision 12148: 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)
- 10:38 PM Revision 12147: schemas/vegbien.sql: public_validation: split into separate subschemas for plots, specimens, traits
- 10:33 PM Revision 12146: schemas/Makefile: vegbien.sql: support auxiliary schemas besides *_validation
- 10:03 PM Revision 12145: 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.
- 10:00 PM Revision 12144: fix: schemas/vegbien.sql: public_validation comment: undid incorrect replacement of "validation" with "public_validation"
- 09:59 PM Revision 12143: bugfix: schemas/Makefile: "public": dont
- 09:37 PM Revision 12142: schemas/Makefile: %/publish: don't ignore errors if schema doesn't exist, because it should always exist if you are publishing it
- 09:36 PM Revision 12141: 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
- 09:34 PM Revision 12140: schemas/Makefile: `%/install: vegbien.sql`: support auxiliary schemas besides *_validation
- 09:16 PM Revision 12139: 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
- 03:55 PM Revision 12138: schemas/vegbien.sql: added rm(), which deletes this schema
- 03:17 PM Revision 12137: schemas/vegbien.sql: added publish(), which publishes this schema
- 02:47 PM Revision 12136: schemas/vegbien.sql: added public_schema_publish()
- 02:21 PM Revision 12135: schemas/util.sql: added functions for maintaining schema bundles, groups of schemas with a common prefix
- 04:26 AM Revision 12134: schemas/util.sql: added schema_bundle_get_schemas()
02/07/2014
- 11:36 PM Revision 12133: schemas/util.sql: added schema_replace()
- 11:11 PM Revision 12132: schemas/util.sql: added schema_rm(), schema_rename()
- 08:30 PM Revision 12131: 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)
- 06:58 PM Revision 12130: bugfix: schemas/Makefile,vegbien.sql: renamed validation to public_validation to match the suffixed name applied by `make schemas/public/install`
- 05:58 PM Revision 12129: schemas/Makefile: %/install, %/publish for public schema: added usage
- 08:37 AM Revision 12128: /README.TXT: to back up the version history: added back `git svn fetch` so we keep the git export up-to-date, too
- 08:29 AM Revision 12127: /README.TXT: to back up the version history: added runtimes (1.5 h for the initial svnsync)
- 08:24 AM Revision 12126: /README.TXT: to back up the version history: added trailing /s to dirs
- 08:24 AM Revision 12125: bugfix: /README.TXT: to back up the version history: fixed svn_repo/ path
- 08:16 AM Revision 12124: **/LICENSE.TXT: corrected "it recommended" to "it is recommended"
- 08:12 AM Revision 12123: _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
- 08:10 AM Revision 12122: _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
- 08:09 AM Revision 12121: _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
- 08:00 AM Revision 12120: /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
- 07:59 AM Revision 12119: _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)
- 07:51 AM Revision 12118: **/LICENSE.TXT: disclaimer about things that are not open-source: removed "these are copyright their respective owners", because this is understood
- 07:22 AM Revision 12117: _license/README.TXT: changed "parts" to "components" for clarity
- 07:18 AM Revision 12116: _license/non-open-source/applies_to.txt: UArizona?: added BIEN2/traits_observation_counts.xls
- 06:52 AM Revision 12115: /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
- 05:53 AM Revision 12114: /LICENSE.TXT: parts of the repository that are not open-source: added ,s to clarify the meaning
- 05:39 AM Revision 12113: /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)
- 05:37 AM Revision 12112: fix: inputs/VegBIEN/Redmine/wiki/.htaccess: redirect to new main page when accessed without trailing /
- 05:26 AM Revision 12111: web/BIEN3: redirected to .wiki since the wiki homepage now contains the list of all BIEN3 components
- 05:26 AM Revision 12110: web/links/index.htm: updated to Firefox bookmarks. Quick links: use bien3.vegpath.org to link to the main BIEN3 page
- 05:05 AM Revision 12109: added web/BIEN3 symlink, with .bien3 case-insensitive alias
- 04:44 AM Revision 12108: _license/*/applies_to.txt: added exclusion for "UCSB modifications"
- 04:38 AM Revision 12107: added _license/GPL2.txt.url
- 04:36 AM Revision 12106: /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
- 04:36 AM Revision 12105: _license/*/LICENSE.TXT: documented that the first section of the file is from license.eml.txt in each folder
- 04:33 AM Revision 12104: /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
- 04:23 AM Revision 12103: /LICENSE.TXT: GPL text: include the full range of copyright years
- 04:17 AM Revision 12102: /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.
- 04:02 AM Revision 12101: added issues/ with LICENSE.TXT for the issue tracker (BSD)
- 03:51 AM Revision 12100: wiki/_license/*/: symlink the contents instead of the folders, because the root dir's and wiki's applies_to.txt's will be different
- 03:49 AM Revision 12099: wiki/_license/*/: symlink the contents instead of the folders, because the root dir's and wiki's applies_to.txt's will be different
- 03:45 AM Revision 12098: wiki/LICENSE.TXT: documented what this license refers to (the wiki hosted at https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/)
- 03:43 AM Revision 12097: wiki/LICENSE.TXT: added message about including _license/ when redistributing, as for /LICENSE.TXT
- 03:42 AM Revision 12096: wiki/_license/LICENSE.TXT: replaced with README.TXT as in /_license
- 03:41 AM Revision 12095: 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
- 03:39 AM Revision 12094: /LICENSE.TXT: moved emphasized sections to top
- 03:37 AM Revision 12093: /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
- 03:36 AM Revision 12092: /LICENSE.TXT: documented that the non-open-source files are now listed in _license/non-open-source/applies_to.txt
- 03:33 AM Revision 12091: added _license/non-open-source/applies_to.txt
- 03:24 AM Revision 12090: 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)
- 03:09 AM Revision 12089: added _license/VegBank_schema/applies_to.txt
- 03:02 AM Revision 12088: schemas/VegCore/vegbien_identifier_examples.xlsx: changed to symlink to Brad_Boyle/vegbien_identifier_examples.xlsx, to avoid duplicate copies
- 02:52 AM Revision 12087: added _license/TWiki/ (for inputs/VegBIEN/TWiki/)
- 02:38 AM Revision 12086: added _license/PostgreSQL_config (for schemas/*.conf)
- 02:24 AM Revision 12085: */LICENSE.TXT: GPL: removed divider between the copyright header and license text, since these are part of the same license
- 02:19 AM Revision 12084: _license/ESA/: renamed to VegBank_schema/ because this license applies only to the VegBank schema
- 02:18 AM Revision 12083: _license/README.TXT: merged ¶2 into ¶1
- 02:04 AM Revision 12082: _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.
- 01:52 AM Revision 12081: /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)
- 01:49 AM Revision 12080: /LICENSE.TXT: removed "svn" before "repository" because this would apply equally to a git export of the repository
- 01:47 AM Revision 12079: /LICENSE.TXT: replaced "portions" with "parts" for consistency with the _license/README.TXT wording
- 01:44 AM Revision 12078: _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.
- 01:32 AM Revision 12077: _license/LICENSE.TXT: renamed to README.TXT because this actually contains a description of the folder, not license text
- 01:24 AM Revision 12076: schemas/Makefile: removed no longer used rename/%, rotate. use %/install, %/publish instead to manage public schema versions.
- 01:22 AM Revision 12075: schemas/Makefile: removed no longer needed public/uninstall, which is handled more generally by `%/uninstall: vegbien.sql` instead
- 01:21 AM Revision 12074: schemas/Makefile: `%/uninstall: vegbien.sql`: added support for *_validation schema
- 01:16 AM Revision 12073: schemas/Makefile: %/uninstall: split into 2 rules like for %/install, so that different actions can easily be added for the public schema
- 01:13 AM Revision 12072: schemas/Makefile: %/publish: support auxiliary *_validation schemas
- 01:12 AM Revision 12071: bugfix: schemas/Makefile: `%/install: vegbien.sql`: need -e before each s/// expression
02/06/2014
- 07:34 PM Revision 12070: 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.
- 04:48 PM Revision 12069: 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
- 04:16 PM Revision 12068: validation/aggregating/*/*.sql (the output queries): added `SET search_path TO validation`
- 04:12 PM Revision 12067: validation/aggregating/specimens/qualitative_validations_specimens.sql: added CREATE VIEW prefixes using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW
- 04:11 PM Revision 12066: 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
- 04:03 PM Revision 12065: 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
- 03:47 PM Revision 12064: 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
- 02:48 PM Revision 12063: added validation/aggregating/specimens/qualitative_validations_specimens.sql template, with query descriptions from NY/qualitative_validations_source_db_NYBG.sql
- 02:08 PM Revision 12062: 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.
- 01:56 PM Revision 12061: 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.
- 01:14 PM Revision 12060: inputs/bien2_traits/TraitObservation/postprocess.sql: remove rows with no taxon name, which are invalid, and which helps simplify the aggregating validations queries
- 12:33 PM Revision 12059: added validation/aggregating/pipeline/aggregating_validations_pipeline.odg with .png export
- 11:09 AM Revision 12058: 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.
- 10:57 AM Revision 12057: 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
- 10:49 AM Revision 12056: added validation/aggregating/plots/FIA/
- 03:46 AM Revision 12055: validation/aggregating/*.by=Brad@iPlant*: placed under version control, since these are now open-source
- 03:41 AM Revision 12054: validation/**: removed svn:ignore exclusion of iPlant-owned files, since these are now open-source
- 03:05 AM Revision 12053: fix: inputs/VegBIEN/Redmine/svn/.htaccess: updated repository URL to point to trunk/
- 03:03 AM Revision 12052: 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.
- 02:44 AM Revision 12051: schemas/vegbien.ERD.mwb: regenerated exports
- 02:41 AM Revision 12050: _license/VegBank/: renamed to ESA/ following the convention that each _license/ subfolder is a copyright owner
02/05/2014
- 06:03 PM Revision 12049: /LICENSE.TXT: added collective license conditions (GPL2+) for the svn repository as a whole, except the non-open-source portions
- 05:50 PM Revision 12048: added _license/VegBank/
- 05:24 PM Revision 12047: 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.
- 06:05 AM Revision 12046: schemas/vegbien.ERD.mwb: synced to schemas/vegbien.my.sql, which adds the validation schema
- 05:51 AM Revision 12045: schemas/util.sql: added diff_views()
- 05:31 AM Revision 12044: schemas/util.sql: added diff_cols(), for use with the aggregating validations
- 01:16 AM Revision 12043: 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)
- 01:02 AM Revision 12042: 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.
- 12:55 AM Revision 12041: bugfix: bin/pg_dump_vegbien: fixed arg-count check to allow passing command-line options to pg_dump via args
02/04/2014
- 10:42 AM Revision 12040: bugfix: inputs/SALVIAS/verify/plots.out.sql: fixed ' quoting syntax to use '' instead of \' to escape '
- 10:32 AM Revision 12039: 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.
- 10:01 AM Revision 12038: fix: inputs/CVS/project/: added _no_import since this should not also be imported separately from taxon_observation.**
- 04:21 AM Revision 12037: fix: validation/aggregating/traits/_archive/bien3_validations_traits_bien3.by=Brad@iPlant,Aaron@UCSB,Brad@iPlant.sql: added missing .url extension
02/03/2014
- 05:50 PM Revision 12036: added validation/aggregating/traits/_archive/bien3_validations_traits_bien3.by=Brad@iPlant,Aaron@UCSB,Brad@iPlant.sql
- 05:37 PM Revision 12035: 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)
- 05:32 PM Revision 12034: added validation/aggregating/traits/BIEN2_traits/_archive/bien3_validations_traits_original_mysql.by=Brad@iPlant,Aaron@UCSB,Brad@iPlant.sql.url
- 01:54 AM Revision 12033: validation/aggregating/plots/_archive/bien3_validations_salvias_vegbien.by=Brad@iPlant.sql.url: removed trailing @
- 01:53 AM Revision 12032: deleted validation/aggregating/traits/_archive/bien3_validations_traits_bien3.by=Brad@iPlant.sql.url@, since there is already a version without the trailing @
- 01:48 AM Revision 12031: 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)
02/02/2014
- 11:18 PM Revision 12030: added inputs/XAL/Specimen/_no_import, since this is a demo-only datasource and there isn't a staging table for it
- 11:10 PM Revision 12029: 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)
- 10:31 PM Revision 12028: inputs/FIA/taxon_observation.**/header.csv: updated for new REF_RESEARCH_STATION.country metadata value col
- 10:27 PM Revision 12027: /README.TXT: Full database import: `make test by_col=1`: documented runtime (20 min)
- 10:27 PM Revision 12026: /README.TXT: Full database import: `. bin/import_all`: documented how to view progress
- 09:30 PM Revision 12025: fix: schemas/Makefile: %/uninstall: don't prompt to delete auxiliary schemas, as these do not contain data
- 07:52 PM Revision 12024: schemas/vegbien.sql: added top_plot view
- 06:22 PM Revision 12023: /README.TXT: to back up the version history: added steps to sync the git repository to jupiter and the local machine
- 05:44 PM Revision 12022: /README.TXT: added steps to back up the version history
- 05:30 PM Revision 12021: 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
- 01:57 AM Revision 12020: 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 )
- 01:51 AM Revision 12019: 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.
- 12:49 AM Revision 12018: inputs/input.Makefile: add!: verify/: also svn:ignore *.tsv, *.txt
02/01/2014
- 11:57 PM Revision 12017: validation/aggregating/traits/bien3_validations_traits_bien3.by=Brad@iPlant.sql*: moved to _archive/
- 11:57 PM Revision 12016: validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original.by=Brad@iPlant.sql*: moved to _archive/
01/28/2014
- 05:02 PM Revision 12015: schemas/vegbien.sql: location_set_top_plot(): only do the lookup of the parent's top_plot when there is a parent_id
- 04:56 PM Revision 12014: schemas/vegbien.sql: location: added autopopulated top_plot
01/26/2014
- 11:09 AM Revision 12013: schemas/vegbien.sql: locationevent: added locationevent_pull_forward_from_parent() trigger which populates project_id from the parent locationevent
- 10:23 AM Revision 12012: web/links/index.htm: updated to Firefox bookmarks: NCEAS: added link to phone list, which contains the Balboa Building maintenance numbers
01/25/2014
- 09:18 PM Revision 12011: /README.TXT: Notes on running programs: added warning that you should always start with a clean shell to avoid spurious bugs
- 11:17 AM Revision 12010: schemas/vegbien.sql: locationevent__pull_forward_from_parent(): renamed to locationevent_pull_forward_from_parent_for_stratum() since it actually has a filter that causes it to apply only to stratum events
01/24/2014
- 11:22 PM Revision 12009: added validation/aggregating/, containing folders for Brad's scripts (the scripts themselves cannot be in the repository because they are not UCSB-owned)
- 04:38 PM Revision 12008: web/links/index.htm: updated to Firefox bookmarks: svn: added steps to add a file containing @ (append @ to the path)
01/23/2014
- 03:07 PM Revision 12007: web/links/index.htm: updated to Firefox bookmarks: `mysql`: added commands to get interactive formatting (including echoed queries) when inputting from a file, and to get raw formatting when inputting from the console. git: added equivalent to `svn update`.
- 11:21 AM Revision 12006: bugfix: schemas/vegbien.sql: commconcept: added missing unique constraint on commdescription, which is also an identifying field in addition to the ID (which is in commname.commname)
- 01:44 AM Revision 12005: inputs/publishable datasources.xlsx: updated
- 01:43 AM Revision 12004: inputs/publishable datasources.xlsx: updated
- 01:35 AM Revision 12003: fix: inputs/SALVIAS/projects/postprocess.sql: remove private data that should not be publicly visible: remove projects that do not have "There are no specific use conditions attached to this dataset"
- 01:22 AM Revision 12002: fix: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Remove private data that should not be publicly visible: also need to remove metadata-only plots
- 01:11 AM Revision 12001: bugfix: inputs/SALVIAS/plotMetadata_/map.csv: things mapped to project_participant: remapped to event__participant because these actually relate to the *event*, not the project, even though they seem like project-related fields
- 01:04 AM Revision 12000: mappings/VegCore-VegBIEN.csv: event__participant: allow multiple event__participant columns
- 12:54 AM Revision 11999: fix: inputs/SALVIAS/plotMetadata_/map.csv, inputs/Madidi/LocationObservation/map.csv: things mapped to communityID: remapped to communityName, which is what's used in analytical_stem (communityID is for numeric IDs)
- 12:15 AM Revision 11998: bugfix: schemas/vegbien.sql: locationevent__communities(): inner-join to commdetermination instead of left-joining, so that this does not produce community entries (which occur because there is one commclass per locationevent, but only some commclasses will then have a commdetermination)
01/22/2014
- 11:01 PM Revision 11997: inputs/SALVIAS/plotMetadata_/create.sql, map.csv: expanded plot_administrator:party_code_party_ and mapped plot_administrator_name to a 2nd project_participant
- 10:59 PM Revision 11996: mappings/VegCore-VegBIEN.csv: project_participant: use [!...] negative lookahead assertion so that multiple project_participant columns will properly map to separate projectcontributor rows
- 09:57 PM Revision 11995: fix: lib/Parser.py: syntax_err(): error message: lightened the shade of gray so the boundary between the strings before and after the error would be clearer
- 09:16 PM Revision 11994: inputs/SALVIAS/plotMetadata_/map.csv: mapped PrimOwnerID_name->project_participant
- 09:07 PM Revision 11993: inputs/SALVIAS/plotMetadata_/create.sql: added join to PrimOwnerID:party_code_party_
- 01:06 PM Revision 11992: bugfix: inputs/SALVIAS/import_order.txt: added party_code_party_
- 12:50 PM Revision 11991: bugfix: inputs/SALVIAS/party_code_party_/create.sql: need to remove duplicate entries in party_code_party
- 12:24 PM Revision 11990: schemas/vegbien.sql: projectcontributor: added missing unique constraint
- 12:17 PM Revision 11989: web/links/index.htm: updated to Firefox bookmarks: OS X 10.9 Mavericks upgrade: added links for whether to upgrade (conclusion: *don't*, it breaks existing programs)
- 11:10 AM Revision 11988: inputs/SALVIAS/party_code_party_/map.csv: mapped fullname->event_participant_name for use by other tables
- 10:34 AM Revision 11987: mapped inputs/SALVIAS/party_code_party_/
01/21/2014
- 07:33 PM Revision 11986: planning/resources/dev_machine.specs/sys_info.spx+/system_power_settings.txt: updated: enabled PrioritizeNetworkReachabilityOverSleep
- 07:23 PM Revision 11985: /README.TXT: Testing: added pointer to development machine specs
- 07:22 PM Revision 11984: added planning/resources/dev_machine.specs/
01/20/2014
- 10:12 PM Revision 11983: inputs/SALVIAS/_MySQL/salvias_plots.*.sql: refreshed. this adds the party and party_code_party tables Brad provided for mapping the plot contributors.
- 10:10 PM Revision 11982: fix: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Delete rows that do not satisfy foreign key constraints: also need to do this for plotObservations, since the refreshed data contains dangling rows for that as well
- 10:08 PM Revision 11981: inputs/SALVIAS/run_: documented *.sql install runtime (3 min), as separate from the full `datasrc_make reinstall` runtime (3.5 min)
- 10:07 PM Revision 11980: inputs/SALVIAS/run_: refresh(): `datasrc_make reinstall`: updated runtime. documented that runtimes are from starscream.
- 08:09 PM Revision 11979: added inputs/SALVIAS/run_, which includes a refresh() target
- 07:22 PM Revision 11978: lib/runscripts/in_datasrc_dir.run: datasrc_make(): use `if remaking ...` instead of accessing $_remake manually, for clarity
- 07:17 PM Revision 11977: bugfix: lib/runscripts/in_datasrc_dir.run: datasrc_make(): use set_make_vars and $_remake as required in lib/sh/make.sh `remaking`
- 07:15 PM Revision 11976: lib/sh/make.sh: remaking alias: documented that you *MUST* use set_make_vars at the beginning of any function that uses this, so that $_remake is properly set to $remake and not left at its previous value
- 02:23 PM Revision 11975: web/links/index.htm: updated to Firefox bookmarks. git: added instructions to migrate from svn.
- 02:20 PM Revision 11974: web/links/index.htm: updated to Firefox bookmarks. git: added instructions to migrate from svn.
- 12:01 PM Revision 11973: web/links/index.htm: updated to Firefox bookmarks. added instructions for running `svn switch` after moving everything into /trunk/ (for us, use `svn switch --force https://code.nceas.ucsb.edu/code/projects/bien/trunk # runtime: <1 min`).
- 11:59 AM Revision 11972: web/links/index.htm: updated to Firefox bookmarks. added instructions for running `svn switch` after moving everything into /trunk/ (for us, use `svn switch --force https://code.nceas.ucsb.edu/code/projects/bien/trunk # runtime: <1 min`).
- 11:41 AM Revision 11971: /: re-set svn:ignore on new root (/trunk/)
- 11:33 AM Revision 11970: moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). *IMPORTANT*: do *NOT* do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
- 11:23 AM Revision 11969: added standard svn dirs branches, tags, trunk
01/18/2014
- 11:43 PM Revision 11968: web/links/index.htm: updated to Firefox bookmarks. added links to the sPlot ERD. Dropbox: added information about a missing upgrade notification when you use the Dropbox client to look up a file on the Dropbox website.
- 10:51 PM Revision 11967: /README.TXT: added note that shell scripts should always be read-only, so that editing them while an import is in progress will not crash the import (see http://vegpath.org/links/#**%20modifying%20a%20running%20shell%20script)
01/16/2014
- 11:22 AM Revision 11966: /: svn:ignore the new extern/ dir, which will contain non-UCSB files
- 01:22 AM Revision 11965: bugfix: inputs/.TNRS/schema.sql: scrubbed_family: Name_matched_accepted_family was missing from the TNRS results at one point, so we are now using Family_matched as a workaround to populate this. the workaround is for *accepted names only*, as no opinion names do not have an Accepted_name_family to prepend to the scrubbed name to parse.
- 01:19 AM Revision 11964: inputs/.TNRS/schema.sql: reexported from live DB, which changes the element order
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