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
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.
/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)
/: svn:ignore the new extern/ dir, which will contain non-UCSB files
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.
inputs/.TNRS/schema.sql: reexported from live DB, which changes the element order
schemas/vegbien.sql: plot.**, analytical_stem_view, analytical_plot: added project_contributors
schemas/vegbien.sql: added project_contributors()
inputs/VegBank/import_order.txt: added projectcontributor_
inputs/VegBank/projectcontributor_/map.csv, postprocess.sql: added project_participant
mappings/VegCore-VegBIEN.csv: mapped project_participant
mappings/VegCore.htm: regenerated from wiki. merged confusingly-named TaxonObservation into TaxonOccurrence. added project_participant.
added inputs/VegBank/projectcontributor_/
inputs/VegBank/vegbank.~.clean_up.sql: projectcontributor.surname: prepend table name to avoid join collisions
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
web/links/index.htm: updated to Firefox bookmarks. Quick links: removed page descriptions, which clutter up the quick links list.
web/links/index.htm: updated to Firefox bookmarks. Quick links: added VegBIEN FAQ.
bugfix: bin/boldify: also match [[]]-style links at the beginning and end of a line
bin/boldify: made it idempotent
bugfix: bin/boldify: fixed extended regular expression syntax, which doesn't support a \] inside [] (you instead have to put the ] right after the opening [^ )
added bin/boldify, which makes Redmine links bold
web/links/index.htm: updated to Firefox bookmarks. Quick links: removed page descriptions, which clutter up the quick links list
web/links/index.htm: updated to Firefox bookmarks. Quick links: added link to meetings
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.
web/links/index.htm: updated to Firefox bookmarks. updated favicons.
web/links/index.htm: updated to Firefox bookmarks. added links for sPlot and iPlant open-sourcing.
inputs/datasource_release_status.xlsx: renamed to `publishable datasources.xlsx` to match the spreadsheet title
planning/meetings/BIEN conference call availability.xlsx: updated
/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
fix: planning/timeline/timeline.xls: realigned legend
planning/timeline/timeline.xls: hid previous weeks
planning/timeline/timeline.xls: crossed out and hid completed tasks
planning/timeline/timeline.xls: updated for progress
web/links/index.htm: updated to Firefox bookmarks. open-sourcing BIEN: added links for VegBank's license (GPLv2), and how these terms apply to us (a diff of our changes is not GPL-ed under GPLv2, although it is claimed to be GPL-ed under GPLv3)
inputs/VegBank/^taxon_observation.**.sample/create.sql, map.csv: added new project columns
inputs/VegBank/taxon_observation.**/postprocess.sql: added the project table
mapped inputs/VegBank/project/, which includes the projectName for attribution
inputs/CVS/^taxon_observation.**.sample/create.sql, map.csv: added new project columns
inputs/CVS/taxon_observation.**/postprocess.sql: added the project table
inputs/CVS/project/map.csv: mapped stopDate->projectEndDate
mapped inputs/CVS/project/, which includes the projectName for attribution
inputs/VegBIEN/Redmine/svn/.htaccess: updated to use much faster direct repository URL rather than Redmine web interface, now that the repository itself is publicly accessible in addition to the Redmine view of it
planning/timeline/timeline.2013.xls: renamed to timeline.xls so that this can continue to be used for 2014 (leaving a symlink from the old filename to preserve permalinks)
fix: inputs/TEX/Specimen*/map.csv, postprocess.sql: habitat: also placed in occurrenceRemarks so that this field gets parsed for growth form information, as requested by Brad (wiki.vegpath.org/TEX_validation#2013-2-26)
fix: inputs/TEX/Specimen*/map.csv: mapped constant values for specimenHolderInstitutions, country. these have to be added with `rm=1 ./inputs/TEX/Specimen.../run postprocess`.
bugfix: inputs/TEX/Specimen2/map.csv: mapped BARCODE to accessionNumber so that we have a unique ID for each row
schemas/vegbien.sql: analytical_stem_view: scientificName_verbatim: don't use taxonverbatim.taxonname+author as the scientificName_verbatim if only the author is provided. (this lead to weird scientificName_verbatims that contain just the author.)
inputs/datasource_release_status.xlsx: updated
web/links/index.htm: updated to Firefox bookmarks. added links for fixing the "App Store is temporarily unavailable" error (turn on Spotlight) and modifying a running shell script (unlink it first).
bugfix: bin/map: in_is_db: don't ignore errors when the table does not exist, because these prevent an errexit and allow an import to continue when a staging table is missing. suppressing this error had previously been necessary because metadata-only tables (Source/) used to not have installed staging tables, and the program had to react accordingly.
inputs/CVS/^taxon_observation.**.sample/create.sql: added Mike Lee's additional plots used to validate confidentiality-related fields (wiki.vegpath.org/CVS_validation#plots-to-include)
bugfix: inputs/CVS/^taxon_observation.**.sample/create.sql: include taxonName in the subset of columns that's imported for the validation, because it is _alt-ed with scientificName for forming the TNRS input name. this is unique to CVS, which is why it was not part of the validation subset copied from the VegBank subset.
/README.TXT: Full database import: documented that you should always start with a clean shell, which does not have changes to the env vars. (there have been inexplicable bugs that went away after closing and reopening the terminal window.) note that running `exec bash` is not sufficient to reset the env vars.
fix: lib/sh/util.sh: verbosity_min(): usage: clarified that '' is a special value that causes $verbosity to be overwritten to ''
lib/runscripts/table.run: added test_() target and use it in remake_VegBIEN_mappings() (it would not be clear that remake_VegBIEN_mappings() runs the tests)
bugfix: inputs/.TNRS/schema.sql: granted bien_read SELECT access to derived views as well as the core tnrs table
updated inputs/datasource_release_status.xlsx
added inputs/datasource_release_status.xlsx, export of Google spreadsheet at https://docs.google.com/spreadsheet/ccc?key=0ArZXrTAXd-TYdDRRb2RxYi11TWZrQVh5bVdKOURCeFE
planning/timeline/timeline.2013.xls: updated for progress
