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
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
added validation/aggregating/, containing folders for Brad's scripts (the scripts themselves cannot be in the repository because they are not UCSB-owned)
web/links/index.htm: updated to Firefox bookmarks: svn: added steps to add a file containing (append to the path)
(append
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`.
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)
inputs/publishable datasources.xlsx: updated
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"
fix: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Remove private data that should not be publicly visible: also need to remove metadata-only plots
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
mappings/VegCore-VegBIEN.csv: event__participant: allow multiple event__participant columns
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)
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)
inputs/SALVIAS/plotMetadata_/create.sql, map.csv: expanded plot_administrator:party_code_party_ and mapped plot_administrator_name to a 2nd project_participant
mappings/VegCore-VegBIEN.csv: project_participant: use [!...] negative lookahead assertion so that multiple project_participant columns will properly map to separate projectcontributor rows
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
inputs/SALVIAS/plotMetadata_/map.csv: mapped PrimOwnerID_name->project_participant
inputs/SALVIAS/plotMetadata_/create.sql: added join to PrimOwnerID:party_code_party_
bugfix: inputs/SALVIAS/import_order.txt: added party_code_party_
bugfix: inputs/SALVIAS/party_code_party_/create.sql: need to remove duplicate entries in party_code_party
schemas/vegbien.sql: projectcontributor: added missing unique constraint
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)
inputs/SALVIAS/party_code_party_/map.csv: mapped fullname->event_participant_name for use by other tables
mapped inputs/SALVIAS/party_code_party_/
planning/resources/dev_machine.specs/sys_info.spx+/system_power_settings.txt: updated: enabled PrioritizeNetworkReachabilityOverSleep
/README.TXT: Testing: added pointer to development machine specs
added planning/resources/dev_machine.specs/
inputs/SALVIAS/_MySQL/salvias_plots.*.sql: refreshed. this adds the party and party_code_party tables Brad provided for mapping the plot contributors.
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
inputs/SALVIAS/run_: documented *.sql install runtime (3 min), as separate from the full `datasrc_make reinstall` runtime (3.5 min)
inputs/SALVIAS/run_: refresh(): `datasrc_make reinstall`: updated runtime. documented that runtimes are from starscream.
added inputs/SALVIAS/run_, which includes a refresh() target
lib/runscripts/in_datasrc_dir.run: datasrc_make(): use `if remaking ...` instead of accessing $_remake manually, for clarity
bugfix: lib/runscripts/in_datasrc_dir.run: datasrc_make(): use set_make_vars and $_remake as required in lib/sh/make.sh `remaking`
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
web/links/index.htm: updated to Firefox bookmarks. git: added instructions to migrate from svn.
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`).
/: re-set svn:ignore on new root (/trunk/)
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).
added standard svn dirs branches, tags, trunk
