Activity
From 12/11/2013 to 01/09/2014
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
12/20/2013
- 10:45 PM Revision 11939: fix: planning/timeline/timeline.xls: realigned legend
- 10:44 PM Revision 11938: planning/timeline/timeline.xls: hid previous weeks
- 10:43 PM Revision 11937: planning/timeline/timeline.xls: crossed out and hid completed tasks
- 10:41 PM Revision 11936: planning/timeline/timeline.xls: updated for progress
- 05:41 PM Revision 11935: 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)
- 04:41 PM Revision 11934: inputs/VegBank/^taxon_observation.**.sample/create.sql, map.csv: added new project columns
- 04:31 PM Revision 11933: inputs/VegBank/taxon_observation.**/postprocess.sql: added the project table
- 04:25 PM Revision 11932: mapped inputs/VegBank/project/, which includes the projectName for attribution
- 02:56 PM Revision 11931: inputs/CVS/^taxon_observation.**.sample/create.sql, map.csv: added new project columns
- 02:44 PM Revision 11930: inputs/CVS/taxon_observation.**/postprocess.sql: added the project table
- 02:42 PM Revision 11929: inputs/CVS/project/map.csv: mapped stopDate->projectEndDate
- 02:35 PM Revision 11928: mapped inputs/CVS/project/, which includes the projectName for attribution
- 01:25 AM Revision 11927: 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
- 01:18 AM Revision 11926: planning/timeline/timeline.xls: updated for progress
- 01:13 AM Revision 11925: 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)
- 12:28 AM Revision 11924: 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)
12/19/2013
- 11:49 PM Revision 11923: 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`.
- 11:42 PM Revision 11922: bugfix: inputs/TEX/Specimen2/map.csv: mapped BARCODE to accessionNumber so that we have a unique ID for each row
- 11:11 PM Revision 11921: 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.)
12/17/2013
- 08:06 AM Revision 11920: inputs/datasource_release_status.xlsx: updated
- 07:28 AM Revision 11919: 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).
- 05:47 AM Revision 11918: 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.
12/16/2013
- 07:05 PM Revision 11917: 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)
- 06:00 PM Revision 11916: 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.
- 05:46 PM Revision 11915: /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.
- 04:58 PM Revision 11914: fix: lib/sh/util.sh: verbosity_min(): usage: clarified that '' is a special value that causes $verbosity to be overwritten to ''
- 04:45 PM Revision 11913: 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)
- 01:43 PM Revision 11912: bugfix: inputs/.TNRS/schema.sql: granted bien_read SELECT access to derived views as well as the core tnrs table
12/15/2013
- 05:30 PM Revision 11911: updated inputs/datasource_release_status.xlsx
- 05:27 PM Revision 11910: added inputs/datasource_release_status.xlsx, export of Google spreadsheet at https://docs.google.com/spreadsheet/ccc?key=0ArZXrTAXd-TYdDRRb2RxYi11TWZrQVh5bVdKOURCeFE
12/12/2013
- 08:57 AM Revision 11909: planning/timeline/timeline.2013.xls: updated for progress
- 08:35 AM Revision 11908: bugfix: schemas/vegbien.sql: location: use the place_id from the parent location when no place_id is specified. this fixes a bug in analytical_stem_view where the parent location's place_id was used because it was sometimes missing from the sublocation, but the parent place_id *itself* was sometimes missing instead if sublocations each had their own place information. this way, it is always available directly in the sublocation, populated from the parent location if needed.
- 08:27 AM Revision 11907: bugfix: schemas/vegbien.sql: location: added place_id which is autopopulated from the current locationplace. join on this in plot.**, to avoid a 1:many join when a location has multiple locationplaces.
12/11/2013
- 11:10 PM Revision 11906: bugfix: schemas/vegbien.sql: locationevent_unique_within_parent_by_location unique index: need COALESCE() around location_id since it's nullable
- 10:54 PM Revision 11905: fix: inputs/CVS/^taxon_observation.**.sample/: added _no_import because this table duplicates part of what's imported from taxon_observation.**
- 10:42 PM Revision 11904: bugfix: inputs/VegBank/plot/: added _no_import because this table is left-joined and should not be imported separately
- 10:40 PM Revision 11903: bugfix: inputs/{.NCBI,CTFS}/*.src/: added _no_import because these tables are left-joined and should not be imported separately
- 09:56 PM Revision 11902: inputs/import.stats.xls: removed table names from datasources where only one table is imported
- 09:52 PM Revision 11901: fix: inputs/import.stats.xls: removed deleted tables from current import
- 09:51 PM Revision 11900: inputs/import.stats.xls: updated import times
- 07:56 PM Revision 11899: updated backups/TNRS.backup.md5
- 07:56 PM Revision 11898: added backups/vegbien.r11786.backup.md5
- 07:53 PM Revision 11897: /README.TXT: Full database import: backups: added step to download backup to local machine
- 07:45 PM Revision 11896: bugfix: /Makefile: install: need to run inputs/download in live mode so that the flat files are actually downloaded
- 07:43 PM Revision 11895: lib/common.Makefile: added %/live, for use with `make inputs/download`
Also available in: Atom