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  • svn:ignore: extern

# Date Author Comment
12058 02/06/2014 11:09 AM Aaron Marcuse-Kubitza

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.

12057 02/06/2014 10:57 AM Aaron Marcuse-Kubitza

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

12056 02/06/2014 10:49 AM Aaron Marcuse-Kubitza

added validation/aggregating/plots/FIA/

12055 02/06/2014 03:46 AM Aaron Marcuse-Kubitza

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

12054 02/06/2014 03:41 AM Aaron Marcuse-Kubitza

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

12053 02/06/2014 03:05 AM Aaron Marcuse-Kubitza

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

12052 02/06/2014 03:03 AM Aaron Marcuse-Kubitza

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.

12051 02/06/2014 02:44 AM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: regenerated exports

12050 02/06/2014 02:41 AM Aaron Marcuse-Kubitza

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

12049 02/05/2014 06:03 PM Aaron Marcuse-Kubitza

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

12048 02/05/2014 05:50 PM Aaron Marcuse-Kubitza

added _license/VegBank/

12047 02/05/2014 05:24 PM Aaron Marcuse-Kubitza

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.

12046 02/05/2014 06:05 AM Aaron Marcuse-Kubitza

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

12045 02/05/2014 05:51 AM Aaron Marcuse-Kubitza

schemas/util.sql: added diff_views()

12044 02/05/2014 05:31 AM Aaron Marcuse-Kubitza

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

12043 02/05/2014 01:16 AM Aaron Marcuse-Kubitza

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)

12042 02/05/2014 01:02 AM Aaron Marcuse-Kubitza

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.

12041 02/05/2014 12:55 AM Aaron Marcuse-Kubitza

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

12040 02/04/2014 10:42 AM Aaron Marcuse-Kubitza

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

12039 02/04/2014 10:32 AM Aaron Marcuse-Kubitza

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.

12038 02/04/2014 10:01 AM Aaron Marcuse-Kubitza

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

12037 02/04/2014 04:21 AM Aaron Marcuse-Kubitza

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

12036 02/03/2014 05:50 PM Aaron Marcuse-Kubitza

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

12035 02/03/2014 05:37 PM Aaron Marcuse-Kubitza

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

12034 02/03/2014 05:32 PM Aaron Marcuse-Kubitza

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

12033 02/03/2014 01:54 AM Aaron Marcuse-Kubitza

validation/aggregating/plots/_archive/bien3_validations_salvias_vegbien.by=: removed trailing @

12032 02/03/2014 01:53 AM Aaron Marcuse-Kubitza

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

12031 02/03/2014 01:48 AM Aaron Marcuse-Kubitza

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

12030 02/02/2014 11:18 PM Aaron Marcuse-Kubitza

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

12029 02/02/2014 11:10 PM Aaron Marcuse-Kubitza

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)

12028 02/02/2014 10:31 PM Aaron Marcuse-Kubitza

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

12027 02/02/2014 10:27 PM Aaron Marcuse-Kubitza

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

12026 02/02/2014 10:27 PM Aaron Marcuse-Kubitza

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

12025 02/02/2014 09:30 PM Aaron Marcuse-Kubitza

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

12024 02/02/2014 07:52 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: added top_plot view

12023 02/02/2014 06:22 PM Aaron Marcuse-Kubitza

/README.TXT: to back up the version history: added steps to sync the git repository to jupiter and the local machine

12022 02/02/2014 05:44 PM Aaron Marcuse-Kubitza

/README.TXT: added steps to back up the version history

12021 02/02/2014 05:30 PM Aaron Marcuse-Kubitza

validation/aggregating/plots/bien3_validations_salvias_vegbien.by=: moved to _archive/ so only the most recent version would be in the main plots/ directory

12020 02/02/2014 01:57 AM Aaron Marcuse-Kubitza

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 )

12019 02/02/2014 01:51 AM Aaron Marcuse-Kubitza

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.

12018 02/02/2014 12:49 AM Aaron Marcuse-Kubitza

inputs/input.Makefile: add!: verify/: also svn:ignore *.tsv, *.txt

12017 02/01/2014 11:57 PM Aaron Marcuse-Kubitza

validation/aggregating/traits/bien3_validations_traits_bien3.by=*: moved to _archive/

12016 02/01/2014 11:57 PM Aaron Marcuse-Kubitza

validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original.by=*: moved to _archive/

12015 01/28/2014 05:02 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: location_set_top_plot(): only do the lookup of the parent's top_plot when there is a parent_id

12014 01/28/2014 04:56 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: location: added autopopulated top_plot

12013 01/26/2014 11:09 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: locationevent: added locationevent_pull_forward_from_parent() trigger which populates project_id from the parent locationevent

12012 01/26/2014 10:23 AM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: NCEAS: added link to phone list, which contains the Balboa Building maintenance numbers

12011 01/25/2014 09:18 PM Aaron Marcuse-Kubitza

/README.TXT: Notes on running programs: added warning that you should always start with a clean shell to avoid spurious bugs

12010 01/25/2014 11:17 AM Aaron Marcuse-Kubitza

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

12009 01/24/2014 11:22 PM Aaron Marcuse-Kubitza

added validation/aggregating/, containing folders for Brad's scripts (the scripts themselves cannot be in the repository because they are not UCSB-owned)

12008 01/24/2014 04:38 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: svn: added steps to add a file containing (append to the path)

12007 01/23/2014 03:07 PM Aaron Marcuse-Kubitza

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`.

12006 01/23/2014 11:21 AM Aaron Marcuse-Kubitza

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)

12005 01/23/2014 01:44 AM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

12004 01/23/2014 01:43 AM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

12003 01/23/2014 01:35 AM Aaron Marcuse-Kubitza

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"

12002 01/23/2014 01:22 AM Aaron Marcuse-Kubitza

fix: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Remove private data that should not be publicly visible: also need to remove metadata-only plots

12001 01/23/2014 01:11 AM Aaron Marcuse-Kubitza

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

12000 01/23/2014 01:04 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: event__participant: allow multiple event__participant columns

11999 01/23/2014 12:54 AM Aaron Marcuse-Kubitza

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)

11998 01/23/2014 12:15 AM Aaron Marcuse-Kubitza

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)

11997 01/22/2014 11:01 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/plotMetadata_/create.sql, map.csv: expanded plot_administrator:party_code_party_ and mapped plot_administrator_name to a 2nd project_participant

11996 01/22/2014 10:59 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: project_participant: use [!...] negative lookahead assertion so that multiple project_participant columns will properly map to separate projectcontributor rows

11995 01/22/2014 09:57 PM Aaron Marcuse-Kubitza

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

11994 01/22/2014 09:16 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/plotMetadata_/map.csv: mapped PrimOwnerID_name->project_participant

11993 01/22/2014 09:07 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/plotMetadata_/create.sql: added join to PrimOwnerID:party_code_party_

11992 01/22/2014 01:06 PM Aaron Marcuse-Kubitza

bugfix: inputs/SALVIAS/import_order.txt: added party_code_party_

11991 01/22/2014 12:50 PM Aaron Marcuse-Kubitza

bugfix: inputs/SALVIAS/party_code_party_/create.sql: need to remove duplicate entries in party_code_party

11990 01/22/2014 12:24 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: projectcontributor: added missing unique constraint

11989 01/22/2014 12:17 PM Aaron Marcuse-Kubitza

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)

11988 01/22/2014 11:10 AM Aaron Marcuse-Kubitza

inputs/SALVIAS/party_code_party_/map.csv: mapped fullname->event_participant_name for use by other tables

11987 01/22/2014 10:34 AM Aaron Marcuse-Kubitza

mapped inputs/SALVIAS/party_code_party_/

11986 01/21/2014 07:33 PM Aaron Marcuse-Kubitza

planning/resources/dev_machine.specs/sys_info.spx+/system_power_settings.txt: updated: enabled PrioritizeNetworkReachabilityOverSleep

11985 01/21/2014 07:23 PM Aaron Marcuse-Kubitza

/README.TXT: Testing: added pointer to development machine specs

11984 01/21/2014 07:22 PM Aaron Marcuse-Kubitza

added planning/resources/dev_machine.specs/

11983 01/20/2014 10:12 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/_MySQL/salvias_plots.*.sql: refreshed. this adds the party and party_code_party tables Brad provided for mapping the plot contributors.

11982 01/20/2014 10:10 PM Aaron Marcuse-Kubitza

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

11981 01/20/2014 10:08 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/run_: documented *.sql install runtime (3 min), as separate from the full `datasrc_make reinstall` runtime (3.5 min)

11980 01/20/2014 10:07 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/run_: refresh(): `datasrc_make reinstall`: updated runtime. documented that runtimes are from starscream.

11979 01/20/2014 08:09 PM Aaron Marcuse-Kubitza

added inputs/SALVIAS/run_, which includes a refresh() target

11978 01/20/2014 07:22 PM Aaron Marcuse-Kubitza

lib/runscripts/in_datasrc_dir.run: datasrc_make(): use `if remaking ...` instead of accessing $_remake manually, for clarity

11977 01/20/2014 07:17 PM Aaron Marcuse-Kubitza

bugfix: lib/runscripts/in_datasrc_dir.run: datasrc_make(): use set_make_vars and $_remake as required in lib/sh/make.sh `remaking`

11976 01/20/2014 07:15 PM Aaron Marcuse-Kubitza

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

11975 01/20/2014 02:23 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. git: added instructions to migrate from svn.

11974 01/20/2014 02:20 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. git: added instructions to migrate from svn.

11973 01/20/2014 12:01 PM Aaron Marcuse-Kubitza

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`).

11972 01/20/2014 11:59 AM Aaron Marcuse-Kubitza

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`).

11971 01/20/2014 11:41 AM Aaron Marcuse-Kubitza

/: re-set svn:ignore on new root (/trunk/)

11970 01/20/2014 11:33 AM Aaron Marcuse-Kubitza

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).

11969 01/20/2014 11:23 AM Aaron Marcuse-Kubitza

added standard svn dirs branches, tags, trunk