Activity
From 01/08/2014 to 02/06/2014
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.
- 09:14 PM Task #859 (New): fix slowness in _taxonlabel_set_parent_id()
- occurs when doing a full import of NCBI:...
- 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
- 10:40 AM Task #857 (New): standardize taxon ranks to a common vocabulary
- _requested by Mike Lee:_
> Betula lenta fo. lenta
>
> The fo. seems odd to me.
>
> Then subsp. is used inste... - 10:23 AM Task #856 (New): data provider feedback tables: include the individual records that have errors
- _this has been specifically requested by Peter Jorgensen_
* add a column with a list of associated record IDs
f... - 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
01/15/2014
- 11:23 AM Revision 11963: schemas/vegbien.sql: plot.**, analytical_stem_view, analytical_plot: added project_contributors
- 11:14 AM Revision 11962: schemas/vegbien.sql: added project_contributors()
- 10:18 AM Revision 11961: inputs/VegBank/import_order.txt: added projectcontributor_
- 10:11 AM Revision 11960: inputs/VegBank/projectcontributor_/map.csv, postprocess.sql: added project_participant
- 10:08 AM Revision 11959: mappings/VegCore-VegBIEN.csv: mapped project_participant
- 10:07 AM Revision 11958: mappings/VegCore.htm: regenerated from wiki. merged confusingly-named TaxonObservation into TaxonOccurrence. added project_participant.
- 09:41 AM Revision 11957: added inputs/VegBank/projectcontributor_/
- 09:29 AM Revision 11956: inputs/VegBank/vegbank.~.clean_up.sql: projectcontributor.surname: prepend table name to avoid join collisions
- 09:23 AM Revision 11955: inputs/VegBank/vegbank.~.clean_up.sql, inputs/CVS/cvs.~.clean_up.sql: Prevent "column name specified more than once" errors when tables are joined: put tables in alphabetical order for consistency
- 08:36 AM Revision 11954: web/links/index.htm: updated to Firefox bookmarks. Quick links: removed page descriptions, which clutter up the quick links list.
- 08:34 AM Revision 11953: web/links/index.htm: updated to Firefox bookmarks. Quick links: added VegBIEN FAQ.
- 08:16 AM Revision 11952: bugfix: bin/boldify: also match [[]]-style links at the beginning and end of a line
- 08:11 AM Revision 11951: bin/boldify: made it idempotent
- 08:08 AM Revision 11950: bugfix: bin/boldify: fixed extended regular expression syntax, which doesn't support a \] inside [] (you instead have to put the ] right after the opening [^ )
- 07:59 AM Revision 11949: added bin/boldify, which makes Redmine links bold
01/14/2014
- 09:30 PM Revision 11948: web/links/index.htm: updated to Firefox bookmarks. Quick links: removed page descriptions, which clutter up the quick links list
- 09:28 PM Revision 11947: web/links/index.htm: updated to Firefox bookmarks. Quick links: added link to meetings
- 09:14 PM Revision 11946: web/links/index.htm: updated to Firefox bookmarks. Quick links: reordered in the order they should apper to visitors to the BIEN links page, rather than to me in the bookmarks toolbar.
- 09:04 PM Revision 11945: web/links/index.htm: updated to Firefox bookmarks. updated favicons.
- 08:56 PM Revision 11944: web/links/index.htm: updated to Firefox bookmarks. added links for sPlot and iPlant open-sourcing.
- 08:34 PM Revision 11943: inputs/publishable datasources.xlsx: updated
- 08:31 PM Revision 11942: inputs/datasource_release_status.xlsx: renamed to `publishable datasources.xlsx` to match the spreadsheet title
01/09/2014
- 01:38 AM Revision 11941: planning/meetings/BIEN conference call availability.xlsx: updated
- 12:31 AM Revision 11940: /README.TXT: to synchronize a Mac's settings with my testing machine's: added step to remove the downloaded Spam folder, because spam e-mails often contain viruses that would trigger clamscan
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